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MNE software User`s Guide - Martinos Center for Biomedical Imaging

1. 000s 3 3 Cortical surface reconstruction with FreeSurfer 3 4 Setting up the anatomical MR images for MRilab 3 5 Setting up the source space 000 cece ee eees 3 6 Creating the BEM model meshes Setting up the triangulation files 00000 eae 3 7 Setting up the boundary element model 3 8 Setting up the MEG EEG analysis directory 3 9 Preprocessing the raw data 0000 ce eee eee Cleaning the digital trigger channel 5 Fixing channel information 0 000 eee ee eee Designating bad channels 0000 cece eee eee Downsampling the MEG EEG data 0005 Off line averaging 3 10 Aligning the coordinate frames 0 000000es 3 11 Computing the forward solution 00005 3 12 Setting up the noise covariance matrix 3 13 Calculating the inverse operator decomposition 3 14 Analyzing the data Chapter 4 Processing raw data 4 1 Overview 4 2 Command line options 0 020 e eee eee Common options Interactive mode options 2 0000 eee eee eee Batch mode options 4 3 The user interface 4 4 The File menu Open Open evoked MSH MNE Save 0 ee ee ee ee eee ee ne 51 Change working directory 0000 cece eee eee 51 Read projection annaa aaaea ee eo teeeeeceaetaees 51
2. 0 0 0 eee eee 310 12 12 The forward solution 0000 eee ees 310 12 13 The inverse operator decomposition 311 12 14 Interactive analysis 00 00 c eee ee 312 Getting started 0 a eee 312 Load surfaces 2 2eceuxeseeeestae bss desoreeuece aeeau 312 Load the data ayiceshcupew eae sede debe heneeg sean esos 312 Show field and potential maps 00000 ee 312 Show current estimates 0 000 cee eee 313 Labels and timecourseS 2 00 c eee ees 313 MOFOMING cau one gee hou ees tetee yu eeawe eee geese coe 313 Chapter 13 Useful reading 315 13 1 General MEG reviews 000 cee es 315 13 2 Cortical surface reconstruction and morphing 315 13 3 Forward modeling 00 cece eee 315 13 4 Signal space projections 00 cee eee 316 13 5 Minimum norm estimates 00 00 ee eee ees 316 13 6 fMRI weighted estimates 000 eee eee 317 Appendix A Creating the BEM meshes 319 A 1 Using the watershed algorithm 00e0eeeee 319 A 2 Using FLASH images 000 c cee 320 Organizing MRI data into directories 005 320 Creating the surface tessellations 0005 321 Inspecting the meshes 0 0 eee ee eee 322 A 3 USING seglab 2cescc2 se een nee enewe doc ee eee et ne 24 322 A A USING BrainSuite 2 04200 ie eee ee wee ewe ewe de oe 323 Appendix B Setup at the Martinos Center 325 B 1
3. tomri By default the coordinates are transformed from MRI coordinates to MEG head coordinates This option reverses the transformation to be from MEG head coordinates to MRI coordinates 11 12 Inquiring and changing baselines The utility mne_change_baselines computes baseline values and applies them to an evoked response data file The command line options are version Show the program version and compilation date help List the command line options In lt name gt Specifies the input data file set lt number gt The data set number to compute baselines from or to apply base lines to If this option is omitted all average data sets in the input file are processed 0Ut lt name gt The output file MSH MNE Miscellaneous utilities 11 MSH MNE 11 13 11 13 1 11 13 2 baselines lt name gt Specifies a text file which contains the baseline values to be applied Each line should contain a channel name colon and the baseline value given in native units T m T or V If this option is encoun tered the limits specified by previous bmin and bmax options will not have an effect list lt name gt Specifies a text file to contain the baseline values Listing is pro vided only if a specific data set is selected with the set option bmin lt value ms gt Lower limit of the baseline Effective only if baselines option is not present Both bmin and bmax must be present to co
4. cales Colors Derivations selection Full view layout Projection Compensation Averaging preferences Figure 4 4 The contents of the Adjust menu The contents of the Adjust menu is shown in Figure 4 4 This menu allows the manipulation of various settings of the program 4 5 1 Filter Selecting Filter from the Adjust menu pops up the dialog shown in Figure 4 5 Adjust filter Filter settings Highpass Hz i Lowpass Hz jan Lowpass transition Hz 50 Filter active JK Apply Cancel Help C Figure 4 5 The filter adjustment dialog The items in the dialog have the following functions Highpass Hz The half amplitude point of the highpass filter The width of the transition from zero to one can be specified with the high passw command line option see Section 4 2 Lowest feasible highpass value is constrained by the length of the filter and sampling frequency You will be informed when you press OK or Apply 1f the 54 MSH MNE Processing raw data 4 selected highpass could not be realized The default value zero means no highpass filter 1s applied in addition to the analog high pass present in the data Lowpass Hz The half amplitude point of the lowpass filter Lowpass transition Hz The width of the cos shaped transition from one to zero centered at the Lowpass value Filter active Selects whether or not the filter is applied to the data The filter
5. 0 0 cee eee 345 Matlab toolbox nananana aaa 345 New utilities 0 ee ee es 345 mne_collect_transformS 0 0 eee eee 345 mne_convert_dig_data 0 cece eee 345 mne_edf2fiff oa ares a ere Sew ae Bo ew ew Sew hal whe 346 mne_brain_vision2fiff 0 eee 346 mne_anonymize cou be cheoecaea He eeeeeueneoue ne as 346 mne_opengl_test 0 0c eee 346 mne_volume_data2mri 00 ee ee 346 mne_volume_source_Space 000 eee 346 mne_copy_processing_history 00000 eee 346 D 4 Release notes for MNE software 2 7 347 Software engineering 0 ee 347 Maap lOO saeara sereen die due Gad se pe eudaees awe 347 mne_browse_raW cc ee ee 347 NG ANA ZG amp cau ces weeeee ae dthe es oe ee ee TEESE 348 Miscellaneous 0 0 ee ees 348 Appendix E Licence agreement 349 E 1 License agreement 0 000 cece eee eee eee 349 MSH MNE CHAPTER 1 MSH MNE Introduction This document describes a set of programs for preprocessing and averag ing of MEG and EEG data and for constructing cortically constrained minimum norm estimates This software package will in the sequel referred to as MNE software The software is based on anatomical MRI processing forward modelling and source estimation methods published in Dale Fischl H m l inen and others The software depends on ana tomical MRI processing tools provided by the FreeSurfer software
6. Chapter 2 of this manual gives an overview of the software modules included with MNE software Chapter 3 is a concise cookbook describing a typical workflow for a novice user employing the convenience scripts as far as possible Chapters 4 to 11 give more detailed information about the software modules Chapter 12 discusses processing of the sample data set included with the MNE software Chapter 13 lists some useful back ground material for the methods employed in the MNE software Appendix A is an overview of the BEM model mesh generation methods Appendix B contains information specific to the setup at Martinos Center of Biomedical Imaging Appendix C is a software installation and config uration guide Appendix D summarizes the software history and Appendix E contains the End User License Agreement Note The most recent version of this manual is available at SMNE ROOT share doc MNE manual lt version gt pdf For the present manual lt version gt 2 7 For definition of the MNE_ ROOT envi ronment variable see Section 2 4 We want to thank all MNE Software users at the Martinos Center and in other institutions for their collaboration during the creation of this soft ware as well as for useful comments on the software and its documenta tion The development of this software has been supported by the NCRR Cen ter for Functional Neuroimaging Technologies P41RR14075 06 the NIH grants 1ROIEB009048 01 ROI EB006385 A101 1RO1 HD407
7. lt common parameters gt def lt covariance definition parameters gt The file may contain arbitrarily many covariance definitions starting with def Warning Due to a bug that existed in some versions of the Neuromag acquisition software the trigger line 8 is incorrectly decoded on trigger channel STI 014 This can be fixed by running mne_fix_stim14 on the raw data file before using mne_browse_raw or mne_process_raw This bug has been fixed in the acquisition software at the Martinos Center on Nov 10 2005 Common parameters The average definition starts with the common parameters They include outfile lt name gt The name of the file where the covariance matrix is to be stores This parameter is mandatory eventfile lt name gt Optional file to contain event specifications This file can be either in fif or text format see Section 4 10 5 The event file format 1s rec ognized from the file name if it ends with fif the file is assumed to be in fif format otherwise a text file is expected If this parameter is present the trigger events in the raw data file are ignored and this event file is consulted instead The event file format is described in Section 4 10 5 81 4 Processing raw data 82 logfile lt name gt This optional file will contain detailed information about the averag ing process In the interactive mode the log information can be viewed from the Manage averages window eradReject
8. since P b t P Uc t 0 The projection operator P is called the signal space projection operator and generally provides considerable rejection of noise suppressing external disturbances by a factor of 10 or more The effectiveness of SSP depends on two factors 1 The basis set b b should be able to characterize the disturbance field patterns completely and 2 The angles between the noise subspace space spanned by b b and the signal vectors b t should be as close to 1 2 as possible If the first requirement is not satisfied some noise will leak through because Pb t 0 If the any of the brain signal vectors b t is close to the noise subspace not only the noise but also the signal will be attenu ated by the application of P and consequently there might by little gain in signal to noise ratio Figure 4 16 demonstrates the effect of SSP on the Vectorview magnetometer data After the elimination of a three dimen sional noise subspace the absolute value of the noise is dampened approximately by a factor of 10 and the covariance matrix becomes diago nally dominant MSH MNE MSH MNE 4 16 2 4 16 3 Processing raw data Since the signal space projection modifies the signal vectors originating in the brain it is necessary to apply the projection to the forward solution in the course of inverse computations This is accomplished by mne_inverse_operator as described in Section 6 4 For more information o
9. Scalp Use the scalp surface instead of the inner skull surface in sphere fit ting If the surface is specified with the surf option this one is irrelevant mritrans lt name gt A file containing a transformation matrix between the MEG head coordinates and MRI coordinates With this option the sphere ori MSH MNE Miscellaneous utilities 11 MSH MNE 11 10 11 10 1 11 10 2 gin will be output in MEG head coordinates Otherwise the output will be in MRI coordinates Computing sensitivity maps Purpose mne_sensitivity_map computes the size of the columns of the forward operator and outputs the result in w files Command line options mne_sensitivity_map accepts the following command line options version Show the program version and compilation date help List the command line options fwd lt name gt Specifies a forward solution file to analyze By default the MEG for ward solution is considered proj lt name gt Specifies a file containing an SSP operator to be applied If neces sary multiple proj options can be specified For map types 4 see below SSP is applied to the forward model data For map types 5 and 6 the effects of SSP are evaluated against the unmodi fied forward model eeg Use the EEG forward solution instead of the MEG one It does not make sense to consider a combination because of the different units of measure For the same reason gradiometers and magnetome
10. Show J MNE A dSPM _ sLORETA _ Nothing Threshold Value histagram Refresh Color scale Options thresh 5 00 Retain sign fmid ooo fax js 00 fmult i temult as _ Retain normal component anly Show scale bar Show comments of smooth steps Time integr ms i E Opacity E OK Apply Cancel Help Figure 7 21 Estimate preferences dialog The optional parameters are 178 MSH MNE Interactive analysis 7 MSH MNE Retain sign With this option the sign of the dot product between the current direction and the cortical surface normal will be used as the sign of the values to be displayed This option yields meaningful data only if a strict or a loose orientation constraint was used in the computa tion of the inverse operator decomposition Retain normal component only Consider only the current component normal to the cortical mantle This option is not meaningful with completely free source orienta tions Show scale bar Show the color scale bar at the lower right corner of the display Show comments Show the standard comments at the lower left corner of the display Time integr ms Integration time for each frame At Before computing the esti mates time integration will be performed on sensor data If the time specified for a frame is f the integration range will be ty At 2 lt t lt t At 2 of smooth steps Before display the data wi
11. The block id of this directory node Table 10 18 The directory structure MSH MNE 265 10 The Matlab toolbox 266 The unique identifier of this node parent_id id The unique identifier of the node this node was derived from Table 10 18 The directory structure ee ae aaae I mo fif file version major lt lt 16 minor machid int32 2 Unique identifier of the computer this id was created on sees o sees i32 o Time since January 1 1970 seconds uSeCs C Time since January 1 1970 microsec onds past secs Table 10 19 The id structure row_names cell The names of associated with the rows This member may be empty col_ names cell The names of associated with the col umns This member may be empty data various The matrix data usually of type single or double Table 10 20 The named matrix structure MSH MNE The Matlab toolbox com int32 ihesoumecosiie amesce source coordinate frame see Table 10 15 Look for entries starting with FIFFV_COORD or FIFFV_ MNE COORD tof int32 The destination coordinate frame trans double 4 4 The 4 by 4 coordinate transformation matrix This operates from augmented position column vectors given in from coordinates to give results in to coordi nates Table 10 21 The trans structure tea in32 00 Cine qupe of Misia ane point Paseblowal type of digitizing point Possible val ues are listed in Table 10 15 Look for
12. A summary of the available routines is provided in Tables 10 1 10 14 The toolbox also contains a set of examples which may be usedful starting points for your own development The names of these functions startwith mne_ex and they are listed in Table 10 14 Important The MNE Matlab Toolbox is compatible with Matlab ver sions 7 0 or later Important The matlab function fiff_setup_read_raw has a significant change The sample numbers now take into account possible initial skip in the file i e the time between the start of the data acquisition and the start of saving the data to disk The first_samp member of the returned struc ture indicates the initial skip in samples If you want your own routines which assume that initial skip has been removed perform identically with the previous version subtract first_samp from the sample numbers you specify to fiff_read_raw_segment Furthermore fiff_setup_read_raw has 203 10 The Matlab toolbox an optional argument to allow reading of unprocessed MaxShield data acquired with the Elekta MEG systems e Pose fiff_ find _evoked Find all evoked data sets from a file fiff_read_bad_channels Read the bad channel list fitf_read_ctf_comp Read CTF software gradient com pensation data fiff_read_evoked Read evoked response data fiff_read_evoked_all Read all evoked response data from a file fiff_read_meas_info Read measurement information fiff_read_mri Read an MRI description fi
13. After these steps you are ready to proceed to the actual analysis MSH MNE The sample data set 12 MSH MNE 12 8 12 8 1 12 8 2 Off line averaging Go to directory SAMPLE MEG sample With help of Section 4 13 familiarize yourself with the averaging script audvis ave Using the averaging script interactively You can invoke an averaging script in mne_browse_raw from Process Average Select the audvis ave script from the file selection box that appears Once averaging is complete you can inspect the details of the averaged responses in the Averages window which appears automatically You can redisplay it from Windows Show averages The window which appears when you select Adjust Manage averages allows you to Select which conditions categories are displayed Change the trace colors Inspect the averaging log Save the averaged data Delete this set of averages mA BWN Re Note If you decide to save the averages in the interactive mode use the name sample audvis ave f fif for the result Using the averaging script in batch mode The batch mode version of mne_browse_raw mne_process_raw can be used for averaging as well Batch mode averaging can be done with the command mne process raw raw sample audvis raw fif lowpass 40 projoff saveavetag ave ave audvis ave The functions of the options are raw Specifies the raw file lowpass Specifies the lowpass filter
14. List the digital trigger channel events to the specified file By default only transitions from zero to a non zero value are listed If multiple raw data files are specified an equal number of event sout options should be present If the file name ends with fif the output will be in fif format otherwise a text event file will be output allevents List all transitions to file specified with the eventsout option events lt name gt Specifies the name of a fif or text format event file see Section 4 10 5 to be associated with a raw data file to be processed If multiple raw data files are specified the number of events options can be smaller or equal to the number of raw data files If it is equal the event filenames will be associated with the raw data files in the order given If it is smaller the remaining raw data files for which an event file 1s not specified will not have an event file associated with them The event file format is recognized from the file name if it ends with 1if the file is assumed to be in fif for mat otherwise a text file is expected ave lt name gt Specifies the name of an off line averaging description file For details of the format of this file please consult Section 4 13 If mul tiple raw data files are specified the number of ave options can be smaller or equal to the number of raw data files If it 1s equal the averaging description file names will be associated with the ra
15. Save projection nanana naana aa ees 51 Apply bad channels aaaea 52 Load events text a nn nanana aaa eee 52 Load events fif 0 0 eee 52 Save events text nnna nnana aaa ee eee 52 Save events fif 2 0 ce ee eee 52 Load derivations 2244 444 desn4 ne des oe eee ee ee ees es 52 Save derivations 0 0 cece ee ees 53 Load channel selections 0 000 eee ee 53 Save channel selections 0 0 00 eee eee ee 53 OUT Sue ecew an neveeeeeeenebeaan ee ee eaaeeeenerraess 54 4 5 The Adjust Menu 00 ee es 54 INGO Sencee eh eGuseueeeeeueses e pebetsesesegeeuess 54 Soele gh 4a4555 404 aR dare ns heme oo aera eee oes 55 COIS E EEEE EEEE EE yea 57 Derivations 1 0 cc eee ees 58 Selection s u4 5 ohooh ee eee se 4ee deeb eoe eee eee nes 59 Full view layout g2 4534446545 024e2e4524Ge5eRbE655 5524 61 POCION sisitan itira Tarer ERER ENS EGRESS 62 Compensation n a aana aaa ee ee eee 63 Averaging preferences 2 00 c ec ees 63 4 6 The Process menu 0c eee es 65 Averaging ao ou ven ge aed oo hee eo eee ee ee oe 65 Estimation of a covariance matrix 000 0c eae 65 Estimation of a covariance matrix from raw data 65 Creating anew SSP operator 2 0 0 0 0 eee 65 4 7 The Windows menu 0000 e eee eee 67 4 8 The Help Menu 0 ce 68 4 9 The raw data display 0 0 cee es 69 Browsing qata 4 o
16. location for the left hemisphere separated by spaces lt Right gt specifies the coordinates of the viewing location for the right hemi sphere lt Left up gt specifies the direction which is pointing up in the image for left hemisphere and 163 Ea Interactive analysis 164 7 8 6 lt Right up gt is the corresponding up vector for the right hemisphere All values are given in a coordinate system where positive x points to the right positive y to the front and positive z up The lengths of the vectors specified for each of the four items do not matter since parallel projection is used and the up vectors will be automatically normalized The up vec tors are usually O O 1 i e pointing to the positive z direction unless the view is directly from above or below or if some special effect is desired The names of viewing orientations should be less than 9 characters long Otherwise the middle pane of the main display will not be able to accom modate all the controls The widths of the main window panes can be adjusted from the squares at the vertical sashes separating the panes Adjusting lighting The scenes shown in the main surface display and the viewer described in Section 7 10 are lit by fixed diffuse ambient lighting and a maximum of eight light sources The states locations and colors of these light sources can be adjusted from the lighting adjustment dialog shown in Figure 7 14 which can be accessed thr
17. yP where M4 is a Sparse matrix with at most three nonzero elements on each row These elements are determined as follows First using the aligned spherical surfaces for each vertex x find the triangle T on the spherical surface of subject A which contains the location x Next find the numbers of the vene a this triangle and set the corresponding elements on the jth row of M4 so that X will be a linear interpola tion between the triangle vertex values reflecting the location X within the triangle It follows from the above definition that in general BA M4 o M 203 8 Morphing and averaging 204 l e A x yg BA yg 4B A 2 even if A _ y BA 4B A 9 i e the mapping is almost a bijection 8 3 About smoothing The current estimates are normally defined only in a decimated grid which iS a Sparse subset of the vertices in the triangular tessellation of the corti cal surface Therefore any sparse set of values is distributed to neighbor ing vertices to make the visualized results easily understandable This procedure has been traditionally called smoothing but a more appropriate name might be smudging or blurring in accordance with similar opera tions in image processing programs In MNE software terms smoothing of the vertex data is an iterative proce dure which produces a blurred image x from the original sparse image x by applying in each iteration step a
18. 8 4 0 0 3 mm 1 16 8mm planar gradiometer Table 5 2 Normal coil descriptions Note If a plus minus sign occurs in several coordinates all MSH MNE possible combinations have to be included 107 a The forward solution a vesenpton o mm we 3013 Vectorview type 2 2 8 4 0 0 3 mm 1 16 8mm planar gradiometer 3022 Vectorview type 1 4 46 45 6 45 0 3 mm 174 magnetometer 3023 Vectorview type 2 4 6 45 6 45 0 3 mm 1 4 magnetometer 3024 Vectorview type 3 4 45 25 5 25 0 3 mm 1 4 magnetometer 2000 An ideal point 1 0 0 0 1 magnetometer 4001 Magnes WH 4 5 75 5 75 0 0 mm 1 4 magnetometer 1 4 4002 Magnes WH 3600 44 5 4 5 0 0 mm axial gradiometer 4 5 4 5 50 0 mm 74 4003 Magnes reference magne 4 7 5 7 5 0 mm 1 4 tometer 4004 Magnes reference gradi 20 20 0 0 mm ometer measuring diago 20 20 135 mm nal gradients p Magnes reference gradi 87 5 20 0 0 mm ometer measuring off We diagonal gradients 47 5 20 0 0 mm 4005 87 5 20 0 0 mm 47 5 20 0 0 mm 5001 CTF 275 axial gradiometer 44 5 4 5 0 0 mm 44 5 4 5 50 0 mm 5002 CTF reference magnetom 4 4 4 0 mm 1 4 eter 6 8 6 0 0 mm Nn Uo CTF reference gradiome ter measuring diagonal gradients 6 8 6 78 6 mm Table 5 2 Normal coil descriptions Note If a plus minus sign occurs in several coordinates all p
19. D 4 5 Miscellaneous e mne_smooth_w was renamed to mne_smooth and can now handle both w and stc files Say mne_ smooth help to find the options e All binaries now reside in MNE_ROOT bin There are no separate bin mne and bin admin directories e mne_anonymize now has the his option to remove the HIS ID of the subject see Section 11 4 7 e mne_check_surface now has the bem and id options to check sur faces from a BEM fif file For details try mne_check_surface help e mne_compute_raw_inverse now has the orignames option see Section 6 6 1 e Added headcoord option to mne_convert_dig_data see Section 9 3 e Added talairach option to mne_make_cor_set see Section 9 8 e Added the morph option to mne_setup_source_space and mne_make_source_space see Sections 3 5 and 5 4 respectively e Added the prefix option to mne_morph_labels see Section 8 5 e Added the blocks and indent options to mne_show_fiff see Section 11 3 e Added the proj option as well as map types 5 and 6 to mne_sensitivity_map see Section 11 10 e Fixed a bug in mne_inverse_operator which caused erroneous calcula tion of EEG only source estimates if the data were processed with Maxfilter software and sometimes caused similar behavior on MEG EEG source estimates 348 MSH MNE APPENDIX E Licence agreement MSH MNE E 1 This appendix includes the terms of the MNE software End User License Agreement EULA License agreement T
20. For more information on SSP see Section 4 16 MSH MNE Processing raw data 4 4 5 8 Compensation Brings up a dialog to select software gradient compensation This over rides the choice made at the open time For details see Section 4 4 1 above 4 5 9 Averaging preferences X Adjust averaging preferences Preferences Starting time ms 200 0 Ending time ms 500 0 Ignore around stimulus ms 10 0 MEG grad rejection fem 2000 0 MEG grad no signal Tem 0 0 MEG mag rejection fT 1 0 MEG mag no signal fT 0 0 EE rejection uW 1 EEG no signal uy oo EOG rejection u 1 0 EOG no signal u 0 0 ECG rejection mW i ECG no signal im oo J Fix trigger skew Done Apply Cancel Help Figure 4 9 Averaging preferences Selecting Averaging preferences from the Adjust menu pops up the dia log shown in Figure 4 9 These settings apply only to the simple averages calculated with help of tools residing just below the main raw data dis play see Section 4 11 These settings are also applied when a covariance matrix 1s computed to create a SSP operator as described in Section 4 6 4 and in the computation of a covariance matrix from raw data see Section 4 6 3 The items in the dialog have the following functions Starting time ms Beginning time of the epoch to be averaged relative to the trigger Ending time ms Ending time of the epoch to be averaged MSH MNE 63 4 Proc
21. Load surface patch Load a curved or flattened surface patch see Section 7 8 Load morphing surface patch Load a curved or flattened surface patch for morphing see Section 7 9 Load digitizer data Load digitizer data for coordinate frame alignment see Section 7 16 MSH MNE Interactive analysis a View continuous HPI data Load a data file containing continuous head position information see Section 7 17 Manage overlays Bring up the overlay manager to import data from stc and w files see Section 7 14 Save bad channel selection Save the current bad channel selection created in the topographical data display see Section 7 7 Quit Quit the program 7 4 2 The Adjust menu The contents of the Adjust menu is shown in Figure 7 3 Adjust Windows La Scales Estimates select trace layout Lights Field mapping Coordinate alignment Figure 7 3 The Adjust menu Scales Adjust the scales of the data display Estimates Adjust the properties of the displayed current estimates see Section 7 12 Select trace layout Select the layout for the topographical display see Section 7 7 Lights Adjust the lighting of the scenes in the main display and the viewer see Sections 7 12 and 7 10 Field mapping Adjust the field mapping preferences see Section 7 11 Coordinate alignment Establish a coordinate transformation between the MEG and MRI coordi
22. MSH MNE 11 4 7 Removing identifying information Depending no the settings during acquisition in the Elekta Neuromag EEG MEG systems the data files may contain subject identifying infor mation in unencrypted form The utility mne_anonymize was written to clear tags containing such information from a fif file Specifically this utility removes the following tags from the fif file FIFF_SUBJ_FIRST_NAME FIFF_SUBJ_MIDDLE_NAME FIFF_SUBJ_LAST_NAME FIFF SUBJ BIRTH DAY Birthday of the subject Julian day number FIFF_SUBJ_HAND FIFF_SUBJ_WEIGHT FIFF_SUBJ_HEIGHT FIFF_SUBJ_COMMENT Table 11 2 Tags cleared by mne_anonymicze Important mne_anonymize normally keeps the FIFF_SUBJ_HIS_ID tag which can be used to identify the subjects uniquely after the information listed in Table 11 2 have been removed If the his option is specified on the command line the FIFF_SUBJ_HIS_ID tag will be removed as well The data of the tags listed in Table 11 2 and the optional FIFF_SUBJ_HIS_ID tag are overwritten with zeros and the space claimed by omitting these tags is added to the free space list of the file Therefore after mne_anonymize has processed a data file there 1s no way to recover the removed information Use this utility with caution mne_anonymize recognizes the following command line options version Show the program version and compilation date help List the command line options his Remove the FIFF_SUBJ_HIS_ID tag as we
23. The reason for this can be displayed through this help menu item 7 5 Loading data When you select Open from the File menu the data loading dialog shown in Figure 7 8 appears It has four sections 1 A standard file selection box 2 List of available data sets This part is automatically filled in when a proper data file is selected from the file list You can select one or more data sets from this list Multiple selection works with help of the shift and control keys If multiple data sets are selected the data set to be analyzed can be changed from the data set list accessible through Switch to data set in the File menu 3 List of available inverse operator decompositions in the current direc tory and its subdirectory called inv 4 List of options a MRI head transform source specifies a file to read the MRI MEG coordinate transformation information from This is usually the inverse operator file However you can also load data with inverse operator set to lt none gt to view the data as well as field and potential maps derived thereof In this case you need to specify the coordinate transformation file using the Select button usually located in mri Tl neuromag sets under the subject s FreeSurfer direc tory The Default button uses the default transformation file which must be called SSUBJECTS DIR SSUBJECT bem SUBJECT trans fif This can be one of the MRI description files in mri 152 MSH MNE Interactive ana
24. The utility mne_add_triggers modifies the digital trigger channel STI 014 in raw data files to include additional transitions Since the raw data file is modified it is possible to make irreversible changes Use this utility with caution It is recommended that you never run mne_add_triggers on an original raw data file 11 4 6 2 Command line options mne_add_triggers accepts the following command line options version Show the program version and compilation date help List the command line options raw lt name gt Specifies the raw data file to be modified trg lt name gt Specifies the trigger line modification list This text file should con tain two entries per line the sample number and the trigger number to be added into the file The number of the first sample in the file 1s zero It is recommended that trigger numbers whose binary equiva lent has lower eight bits equal to zero are used to avoid conflicts with the ordinary triggers occurring in the file delete Delete the triggers defined by the trigger file instead of adding them This enables changing the file to its original state provided that the trigger file is preserved Note Since mne_browse_raw and mne_process_raw can employ an event file which effectively adds new trigger instants mne_add_triggers is for the most part obsolete but it has been retained in the MNE software suite for backward compatibility MSH MNE Miscellaneous utilities 11
25. W Belliveau and S M Stufflebeam Spectral spatiotemporal imaging of cortical oscilla tions and interactions in the human brain Neuroimage vol 23 pp 582 95 2004 317 13 Useful reading 318 MSH MNE appenpIx A Creating the BEM meshes MSH MNE A 1 Using the watershed algorithm The watershed algorithm Segonne et al 2004 is part of the FreeSurfer software The name of the program is mri_watershed Its use in the MNE environment is facilitated by the script mne_watershed_bem which assumes the following options subject lt subject gt Defines the name of the subject This can be also accomplished by setting the SUBJECT environment variable overwrite Overwrite the results of previous run of mne_watershed_bem atlas Makes mri_watershed to employ atlas information to correct the segmentation After mne_watershed_bem has completed the following files appear in the subject s bem watershed directory lt subject gt _brain_surface Contains the brain surface triangulation lt subject gt _inner_skull_surface Contains the inner skull triangulation lt subject gt _outer_skull_surface Contains the outer skull triangulation lt subject gt _outer_skin_surface Contains the scalp triangulation All of these surfaces are in the FreeSurfer format In addition there will be a directory called bem watershed ws which contains the brain MRI volume Furthermore mne_watershed_bem script converts the scalp s
26. and 4 The noise normalized estimates see Section 6 2 6 Fortunately the latter two are least likely to be affected due to regulariza tion of the estimates However in some cases especially the EEG part of the noise covariance matrix estimate can be deficient i e it may possess very small eigenvalues and thus regularization of the noise covariance matrix is advisable The MNE software accomplishes the regularization by replacing a noise covariance matrix estimate C with C Dea p 123 6 The current estimates 124 where the index k goes across the different channel groups MEG planar gradiometers MEG axial gradiometers and magnetometers and EEG are the corresponding regularization factors are the average variances across the channel groups and I are diagonal matrices containing ones at the positions corresponding to the channels contained in each channel group The values can be adjusted with the regularization options magreg gradreg and eegreg specified at the time of the inverse operator decomposition see Section 6 4 The convenience script mne_do_inverse_solution has the magreg and gradreg combined to a sigle option megreg see Section 3 13 Suggested range of values for is 0 05 0 2 6 2 5 Computation of the solution The most straightforward approach to calculate the MNE is to employ expression for the original or whitened inverse operator directly However for comp
27. data to bring the integration points to another coordinate frame Table 10 3 Coordinate transformation utilities Purpose fiff_define_constants Define a structure which contains the constant relevant to fif files fitf_split_name_list Split a colon separated list of names into a cell array of strings Table 10 4 Basic reading routines Funeion Papo fiff_end_block Write a FIFF_END_BLOCK tag fiff_end_file Write the standard closing Table 10 5 Writing routines MSH MNE 255 10 The Matlab toolbox o Fndion Purpose O Table 10 5 Writing routines e Papas fiff_write_evoked Write an evoked response data file fiff_finish_writing_raw Write the closing tags to a raw data file fiff_start_writing raw Start writing raw data file i e write the measurement information fitf_write_dig_file Write a fif file containing digitization data fiff_write_raw_buffer Write one raw data buffer This is used after a call to fiff_start_writing_raw Table 10 6 High level data writing routines 256 MSH MNE The Matlab toolbox 10 mne_add_coil_defs Add coil definitions to an array of channel information Structures mne_load_coil_def Load a coil definition file Table 10 7 Coil definition utilities mne_compensate_to Apply or remove CTF software gradient compensation from evoked response data mne_get_current_comp Get the state of software gradient compensation from measurement info mne_make_compensat
28. eeg options meg After loading the covariance matrix modify it so that only elements corresponding to MEG channels are included eeg After loading the covariance matrix modify it so that only elements corresponding to EEG channels are included 28 1 Miscellaneous utilities 11 9 11 9 1 11 9 2 288 megmag After loading the covariance matrix modify it so that only elements corresponding to MEG magnetometer channels are included meggrad After loading the covariance matrix modify it so that only elements corresponding to MEG planar gradiometer channels are included Important The megmag and meggrad employ the Vectorview channel numbering scheme to recognize MEG magnetometers channel names ending with 1 and planar gradiometers other channels There fore these options are only meaningful in conjunction with data acquired with a Neuromag Vectorview system Fitting a sphere to a surface Purpose The utility mne_fit_sphere_to_surf finds the sphere which best fits a given surface Command line options mne_fit_sphere_to_surf accepts the following command line options version Show the program version and compilation date help List the command line options bem lt name gt A BEM file to use The names of these files usually end with bem fif or bem sol f1if surf lt name gt A FreeSurfer surface file to read This is an alternative to using a surface from the BEM file
29. if the plot window has a differ ent aspect ratio there will be empty space on the sides The viewports define the locations of the individual channels in the plot Each viewport definition consists of lt number gt xg Yo lt width gt lt height gt lt name gt lt name gt where number is a viewport number not used by the MNE software x and y are the coordinates of the lower left corner of the viewport lt width gt and lt height gt are the viewport dimensions and lt name gt is a name of a channel Multiple channel names can be specified by separating them with a colon When a measurement channel name is matched to a layout channel name all spaces are removed from the channel names and the both the layout channel name and the data channel name are converted to lower case In addition anything including and after a hyphen is omitted The latter convention facilitates using CTF MEG system data which has the serial number of the system appended to the channel name with a dash Removal of the spaces is important for the Neuromag Vectorview data because newer systems do not have spaces in the channel names like the original Vectorview systems did Tip The mne_make_eeg_layout utility can be employed to create a layout file matching the positioning of EEG electrodes see Section 11 6 Projection Lists the currently available signal space projection SSP vectors and allows the activation and deactivation of items
30. lt from gt lt to gt lt text gt where lt sample gt is the sample number This sample number takes into account the initial empty space in a raw data file as indicated by the 73 4 Processing raw data 74 FIFF_FIRST_SAMPLE and or FIFF_DATA_SKIP tags in the beginning of raw data Therefore the event file contents are independent of the Keep initial skip setting in the open dialog lt time gt is the time from the beginning of the file to this sample in sec onds lt from gt is the value of the digital trigger channel at lt sample gt 1 lt to gt is the value of the digital trigger channel at lt sample gt lt text gt is an optional annotation associated with the event This com ment will be displayed in the event list and on the message line when you move to an event When an event file is read back the lt sample gt value will be primarily used to specify the time If you want the lt time gt to be converted to the sample number instead specify a negative value for lt sample gt Each event file starts with a pseudo event where both lt from gt and lt to gt fields are equal to zero Warning In previous versions of the MNE software the event files did not contain the initial empty pseudo event In addition the sample num bers did not take into account the initial empty space in the raw data files The present version of MNE software is still backwards compatible with the old version of the event f
31. lt value T m gt Rejection limit for MEG gradiometer channels If the peak to peak amplitude within the extracted epoch exceeds this value on any of the gradiometer channels the epoch will be omitted from the aver age magReject lt value T gt Rejection limit for MEG magnetometer and axial gradiometer chan nels If the peak to peak amplitude within the extracted epoch exceeds this value on any of the magnetometer or axial gradiometer channels the epoch will be omitted from the average eegReject lt value V gt Rejection limit for EEG channels If the peak to peak amplitude within the extracted epoch exceeds this value on any of the EEG channels the epoch will be omitted from the average eogReject lt value V gt Rejection limit for EOG channels If the peak to peak amplitude within the extracted epoch exceeds this value on any of the EOG channels the epoch will be omitted from the average ecgReject lt value V gt Rejection limit for ECG channels If the peak to peak amplitude within the extracted epoch exceeds this value on any of the ECG channels the epoch will be omitted from the average eradFlat lt value T m gt Signal detection criterion for MEG planar gradiometers The peak to peak value of all planar gradiometer signals must exceed this value for the epoch to be included This criterion allows rejection of data with saturated or otherwise dysfunctional channels The default value is zero i e no reject
32. next to the arrows Fasa ada Figure 7 13 Surface controls The display can be also adjusted using keyboard shortcuts which are available once you click in the main surface display with the left mouse button to make it active Arrow keys Rotate the surface by increments specified in degrees in the Adjust View section fe Enlarge the image Reduce the image Return to the default size r Rotate the image one full revolution around z axis using the cur rently specified rotation step This is useful for producing a Sequence of images when automatic image saving is on see Section 7 8 7 161 Ea Interactive analysis 162 S Produces a raster image file which contains a snapshot of the cur rently displayed image For information on snapshot mode see Section 7 8 7 Stops the rotation invoked with the r key see above In addition the mouse wheel or trackball can be used to rotate the image If a trackball is available e g with the Apple MightyMouse the image can be rotated up and down or left and right with the trackball With a mouse wheel the image will rotated up and down when the wheel is rotated Image rotation in the left right direction is achieved by holding down the shift key when rotating the wheel The shift key has the same effect on trackball operation Note The trackball and mouse wheel functionality is dependent on your X server settings On Mac OSX these settings are normally correct by de
33. options in the mne_analyze alignment dialog are used because then the SUBJECTS_DIR SUBJECT directory will be composed of files which are dependent on the subjects s anatomy only not on the MEG EEG data to be analyzed MSH MNE Interactive analysis a MSH MNE 7 16 1 Each iteration step of the Iterative Closest Point ICP algorithm consists of two matching procedures 1 For each digitizer point transformed from MEG to the MRI coordinate frame using the current coordinate transformation the closest point on the triangulated surface is determined 2 The best coordinate transformation aligning the digitizer points with the closest points on the head surface 1s computed These two steps are iterated the designated number of times If the Try to keep nasion in place option is on the present location of the nasion receives a strong weight in the second part of each iteration step so that nasion movements are discouraged Tip One possible practical approach to coordinate frame alignment is discussed in Section 12 11 Using a high resolution head surface tessellation The newest version of FreeSurfer contains a script called mkheadsurf which can be used for coordinate alignment purposes For more informa tion try mkheadsurf help This script produces a file called surf lh smseghead which can be converted into a fif file using mne_surf2bem Suggested usage Set the SUBJECTS_DIR correctly Run mkheadsurf mkheads
34. see Sections 11 4 3 and 11 4 4 Designating bad channels Sometimes some MEG or EEG channels are not functioning properly for various reasons These channels should be excluded from the analysis by marking them bad using the mne_mark_bad_channels utility see Section 11 4 1 Especially if a channel is not show a signal at all flat it is most important to exclude it from the analysis since its noise estimate will be unrealistically low and thus the current estimate calculations will give a strong weight to the zero signal on the flat channels and will essen tially vanish It is also important to exclude noisy channels because they can possibly affect others when signal space projections or EEG average electrode reference is employed Noisy bad channels can also adversely affect off line averaging and noise covariance matrix estimation by caus ing unnecessary rejections of epochs Recommended ways to identify bad channels are 1 Observe the quality of data during data acquisition and make notes of observed malfunctioning channels to your measurement protocol sheet 2 View the on line averages and check the condition of the channels 3 Compute preliminary off line averages with artefact rejection signal space projection and EEG average electrode reference computation off and check the condition of the channels 4 View raw data in mne_process_raw or the Neuromag signal processor graph without signal space projection or EEG average e
35. shaped pulse centered at t 100 ms with 100 ms leading and trailing slopes 20 nAm amplitude q 30e 9 t gt 0 t lt 300 sin 2 pi 20 x 20 Hz sine wave 30 nAm amplitude cropped in time to 0 300 ms Table 11 5 Examples of source waveform expressions 11 14 Converting parcellation data into labels The utility mne_annot2labels converts cortical parcellation data into a set of labels The parcellation data are read from the directory SSUBJECTS DIR SSUBJECT 1label and the resulting labels are writ ten to the current directory mne_annot2labels requires that the environ ment variable SSUBJECTS DIR is set The command line options for mne_annot2labels are version Show the program version and compilation date help List the command line options subject lt name gt Specifies the name of the subject If this option is not present the SSUBJECT environment variable is consulted If the subject name cannot be determined the program quits parc lt name gt Specifies the parcellation name to convert The corresponding par cellation file names will be SSUBJECTS DIR SSUBJECT label lt hemi gt h lt name gt annot where lt hemi gt is 1 or r for the left and right hemisphere respectively 298 MSH MNE cHAPTER 12 The sample data set MSH MNE 12 1 Purpose This Chapter gives a detailed description of the processing of a sample data set which can be employed to familiarize with the workflow described
36. which will contain the patch area information Two files will be created lt name gt 1lh w and lt name gt rh w The numbers in the files are patch areas in mm The source space verti ces are marked with value 150 MSH MNE Miscellaneous utilities 11 labeldir lt directory gt Create a label file corresponding to each of the patches in the given directory The directory must be created before running mne_add_patch_info 11 8 Converting covariance data into an SSP operator 11 8 1 11 8 2 MSH MNE Purpose The utility mne_cov2proj picks eigenvectors from a covariance matrix and outputs them as a signal space projection SSP file Command line options mne_cov2proj accepts the following command line options yersion Show the program version and compilation date help List the command line options COV lt name gt The covariance matrix file to be used a source The covariance matrix files usually end with cov fif proj lt name gt The output file to contain the projection It is recommended that the file name ends with proj fif bad lt name gt Specify channels not to be included when an eigenvalue decomposi tion of the covariance matrix is computed include lt val gt lt val gt Select an eigenvector or a range of eigenvectors to include It 1s rec ommended that magnetometers gradiometers and EEG data are handled separately with help of the bad meg megmag meggrad and
37. 0 2 eeg Note If you were using a single compartment BEM to compute the for ward solution you can only compute the MEG inverse operator 311 12 The sample data set 312 12 14 12 14 1 12 14 2 12 14 3 12 14 4 Interactive analysis The most exciting part of this exercise is to explore the data and the cur rent estimates in mne_analyze This section contains some useful steps to get you started A lot of information about the capabilities of mne_analyze is given in Chapter 7 Batch mode processing with mne_make_movie 1s discussed in Section 6 5 Cross subject averaging is covered in Chapter 8 Before launching mne_analyze it is advisable to go to the directory MEG sample The current working directory can be also changed from mne_analyze Getting started Launch mne_analyze Select Help On GLX which brings up a window containing Open GL rendering context information If first line in the information dialog that pops up says Nondirect rendering context instead of Direct rendering context you will experience slow graphics perfor mance To fix this your system software graphics adapter or both need to be updated Consult a computer support person for further information Load surfaces It is reasonable to start the analysis by loading the display surfaces choose the inflated surface for subject sample from the dialog that appears when you select File Load surface Load the data Select File Open Sel
38. 2 It reduces the location bias of the estimates In particular the tendency of the MNE to prefer superficial currents is eliminated 3 The width of the point spread function becomes less dependent on the source location on the cortical mantle The point spread is defined as the MNE resulting from the signals coming from a point current source a current dipole located at a certain point on the cortex In practice noise normalization requires the computation of the diagonal elements of the matrix T a i MCM MM With help of the singular value decomposition approach we see directly that Fw T MM VI V Under the conditions expressed at the end of Section 6 2 5 it follows that the t statistic values associated with fixed orientation sources are thus proportional to JL while the F statistic employed with free orientation sources is proportional to L correspondingly Note A section discussing statistical considerations related to the noise normalization procedure will be added to this manual in one of the subse quent releases Note The MNE software usually computes the square roots of the F sta tistic to be displayed on the inflated cortical surfaces These are also pro portional to jee 125 6 The current estimates 126 6 2 7 6 2 8 6 2 9 Predicted data Under noiseless conditions the SNR is infinite and thus leads to A 0 and the minimum norm estimate explains the measured data perfectly Und
39. 282 Command line options 44 lt s k e0ccneaee nee eaaew ed hens 283 Derivation file formats 0 00 0 eee ee eee 283 11 6 Creating a custom EEG layout 000000es 285 PUNDOSC bgt be eee eae ee ae eee eh eee es eee ee eee eke 285 11 7 Adding topology information to a source space 286 PUIDOSC 4s ersari rererere dees shee eee e te eoyede eee 286 Command line options 0 0 ee ee 286 11 8 Converting covariance data into an SSP operator 287 PUIDOSS 25456552265 bee eee Shee S Guus sees ee ewede tes 287 Command line options 0 0 eee 287 11 9 Fitting a sphere to a surface 000 c eee ees 288 Purpose 2s oe aeceebeeeum eared ed ee eee seuhed Gene ssh 288 Command line options 0 0 ee ee 288 11 10 Computing sensitivity maps 00000 289 PUDO O 44 aeuted ee ge eee eugene a suede eeee nes euk eos 289 Command line options 0 eee 289 Available sensitivity mapS 0 000 eee eee 290 11 11 Transforming locations 00 cee ee 291 Purpose 2c 42 bee ee ee hope ee eee eee eee ee eee oe 291 Command line options 0 0 ee ee 291 11 12 Inquiring and changing baselines 0005 292 11 13 Data simulator 6 gc2 ese pe neta eee pee ee eee een 293 PUDO O o o4 bene te eee nen beet seed eeee bee EEEE 293 Command line options 0 00 ee 293 Noise simulation 2euceaduvnbacuea erty seeeeeeeneeeunas 294 Simulated data 2 56 enbencns
40. 4 D 1 5 D 1 6 D 1 7 D 2 D 2 1 336 1 mne_ctf2fiff to convert CTF data to the fif format see Section 9 2 2 2 mne_tufts2fiff to convert EEG data from Tufts university to fif format see Section 9 2 9 The output of the Matlab conversion utilities was changed to use struc tures For details see Sections 9 12 9 7 and 9 13 Matlab tools to import and export w and stc files were added mne_browse_raw Output of decimated and filtered data is now available mne_analyze now fully supports 32 bit integer data found in CTF and new Neuromag raw data files mne_analyze The following changes have been made in mne_analyze 1 Curved and flat surface patches are now supported 2 An iterative coordinate alignment procedure was added see Section 7 16 3 Utility to view continuous HPI information was added see Section 7 17 4 Several small changes and bug fixes were done mne_make_movie The only major change in mne_make_movie is the addition of support for curved and surface patches Averaging The highly inefficient program mne_grand_average has been removed from the distribution and replaced with the combined use of mne_make_movie and a new averaging program mne_average_estimates see Section 8 6 Release notes for MNE software 2 5 Manual The MNE Matlab toolbox is now covered in a separate chapter Change bars are employed to indicate changes in the chapters that existed in the MSH MNE Release not
41. 4 Processing raw data 76 4 12 Topographical data displays Segments of data can shown in a topographical layout in the Full view window which can be requested from the Scale dialog or from the Win dows menu Another similar display is available to show the averaged data The topographical layout to use is selected from Adjust Full view layout which brings up a window with a list of available layouts The default layouts reside in SMNE ROOT share mne mne_analyze lout In addition any layout files residing in SHOME mne lout are listed The format of the layout files is the same as for the Neuromag pro grams xplotter and xfit A custom EEG layout can be easily created with the mne_make_eeg_layout utility see Section 11 6 Several actions can be performed with the mouse in the topographical data display Left button Shows the time and the channel name at the cursor at the bottom of the window Left button drag with shift key Enlarge the view to contain only channels in the selected area Right button Brings up a popup menu which gives a choice of graphics output formats for the current topographical display Best quality is achieved with the Illustrator format This format has the benefit that it is object oriented and can be edited in Adobe Illustrator Middle button Drag and drop graphics to one of the cliplab view areas Note The cliplab drag and drop functionality requires that you have the proprietary Elekta Neuromag
42. 5120 5120 meas sample audvis ave fif This produces an EEG and MEG forward solution with source space points closer than 5 mm to the inner skull surface omitted The source space created in Section 12 5 2 will be employed As the output from this command will indicate The forward solution will be stored in file sample audvis ave oct 6 fwd fif This command uses the three layer BEM model sample 5120 5120 5120 bem sol fif created in Section 12 5 3 If you want to use the single compartment BEM sample 5120 bem sol fif usable for MEG data only say cd SSAMPLE MEG sample mne do forward solution mindist 5 spacing oct 6 meas sample audvis ave fif bem sample 5120 megonly 12 13 The inverse operator decomposition The inverse operator information necessary for the computation of the MNEs and dSPMs is accomplished by the command mne do inverse operator fwd sample audvis ave oct 6 fwd fif depth loose 0 2 meg eeg This produces a depth weighted inverse operator decomposition with loose orientation constraint applied More details on the convenience script mne_do_inverse_operator are provided in Section 3 13 The above command employs both EEG and MEG data To create sepa rate solution for EEG and MEG run the commands mne do inverse operator fwd sample audvis ave oct 6 fwd fif depth loose 0 2 meg and mne do inverse operator fwd sample audvis ave oct 6 fwd fif depth loose
43. BrainSuite tessellation files to MNE software compati ble formats is accomplished with the mne_convert_surface utility covered in Section 9 7 The workflow needed to employ the BrainSuite tessellations is Step 1 Using the mri_convert utility available in FreeSurfer convert an MRI volume to the img Analyze format This volume should be the T1l mgz volume or a volume registered with T1 mgz in Free Surfer mri convert lt volume gt mgz lt volume gt img 323 A Creating the BEM meshes 324 Step 2 Transfer lt volume gt mgz to a location accessible to BrainSuite running on Windows Step 3 Using lt volume gt img as input create the tessellations of scalp outer skull and inner skull surfaces in BrainSuite Step 4 Transfer the dfs files containing the tessellations in the bem direc tory of your subject s FreeSurfer reconstruction Step 5 Go to the bem directory where you placed the two dfs files Using mne_convert_surface convert them to the FreeSurfer surface for mat e g mne convert surface dfs inner skull dfs mghmri mri Tl mgz surf inner skull dfs surf Step 6 Using tkmedit check that the surfaces are correct e g tkmedit f mri Tl mgz surface inner skull dfs surf Step7 Using the mne_reduce_surface function in Matlab reduce the num ber of triangles on the surfaces to 10000 20000 Call the output files outer skin surf outer skull surf and inner skull surf Step 8
44. COR in directory SUBJECTS_DIR SUBJECT mri T 1 neuromag sets is looked up If such a file is present it will be used d If all the above searches fail the script exits with an error message This search sequence is designed to work well with the MEG MRI trans formation files output by mne_analyze see Section 7 16 It is recom mended that trans fif file saved with the Save default and Save options in the mne_analyze alignment dialog are used because then the SUBJECTS_DIR SUBJECT directory will be composed of files which are dependent on the subjects s anatomy only not on the MEG EEG data to be analyzed Tip If the standard MRI description file and BEM file selections are appropriate and the 7 mm source space grid spacing is appropriate only the meas option is necessary If EEG data is not used megonly option should be included Tip If it is conceivable that the current density transformation will be incorporated into the inverse operator specify a source space with patch MSH MNE The Cookbook al MSH MNE information for the forward computation This is not mandatory but saves a lot of time when the inverse operator is created since the patch informa tion does not need to be created at that stage Tip The MEG head to MRI transformation matrix specified with the trans option should be a text file containing a 4 by 4 matrix R11 Rig 13 Xo T En 13 413 Yo R13 R13 13 Zo 0 0 0 I defined so that if
45. If the peak to peak amplitude within the extracted epoch exceeds this value on any of the magnetometer or axial gradiometer channels the epoch will be omitted from the average eegReject lt value V gt Rejection limit for EEG channels If the peak to peak amplitude within the extracted epoch exceeds this value on any of the EEG channels the epoch will be omitted from the average eogReject lt value V gt Rejection limit for EOG channels If the peak to peak amplitude within the extracted epoch exceeds this value on any of the EOG channels the epoch will be omitted from the average ecgReject lt value V gt Rejection limit for ECG channels If the peak to peak amplitude within the extracted epoch exceeds this value on any of the ECG channels the epoch will be omitted from the average eradFlat lt value T m gt Signal detection criterion for MEG planar gradiometers The peak to peak value of all planar gradiometer signals must exceed this value for the epoch to be included This criterion allows rejection of data with saturated or otherwise dysfunctional channels The default value is zero i e no rejection magFlat lt value T gt Signal detection criterion for MEG magnetometers and axial gradi ometers channels eegF lat lt value V gt Signal detection criterion for EEG channels eogFlat lt value V gt Signal detection criterion for EOG channels MSH MNE Processing raw data 4 MSH MNE ecgFlat
46. Interacting with mne_analyZe 000 eee ees 91 Chapter 5 The forward solution 93 5 1 Overview ce ees 93 5 2 MEG EEG and MRI coordinate systems 93 5 3 The head and device coordinate systems 97 5 4 Creating a surface based source space 98 5 5 Creating a volumetric or discrete source space 99 5 6 Creating the BEM meshes 000 cee e eens 101 Command line options 0 0 ee ee 101 Surface Options aaa 0a008044 544 oe cee re aew een cases 102 Tessellation file format 0 0 0 0 103 Topology checkS 22 nc6escecaneeaeesaeeaweenaruen ss 104 5 7 Computing the BEM geometry data 5 104 5 8 Coil geometry information 0 00 ee 105 The sensor coordinate system 0 000 eee ees 105 Calculation of the magnetic field 004 106 Implemented coil geometries 00 cee ees 107 The coil definition file 0 0 0 0 0 ccc ees 111 Creating the coil definition file 000005 113 5 9 Computing the forward solution 02 00000e 113 PUIDOSC sssrin EAEE eee oe oe eee ana eee ae eoee oe Se 113 Command line options 0 ee ee 113 Implementation of software gradient compensation 116 The EEG sphere model definition file 116 EEG forward solution in the sphere model 117 Field derivatives 0 0 0 ccc ees 117 5 10 Averaging forward s
47. MSH MNE 7 8 5 MNI Talairach Shows the location in MNI Talairach coordinates To be present the MRI data of the subject must be in the mgz format usually true with any recent FreeSurfer version and the Talairach transforma tion must be appropriately defined during the FreeSurfer reconstruc tion workflow Talairach Shows the location in the FreeSurfer Talairach coordinates which give a better match to the Talairach atlas The above coordinate systems are discussed in detail in Section 5 2 Note By default the tksurfer program part of the FreeSurfer package shows the vertex locations on the orig rather than white surfaces There fore the coordinates shown in mne_analyze and tksurfer are by default slightly different usually by lt mm To make the two programs consis tent you can start tksurfer with the orig white option Defining viewing orientations The list of viewing orientations available in the Adjust View section of the main surface display is controlled by a text file The system wide defaults reside in SMNE_ROOT share mne mne_analyze eyes If the file SHOME mne eyes exists it is used instead All lines in the eyes file starting with are comments The view orienta tion definition lines have the format lt name gt lt Left gt lt Right gt lt Left up gt lt Right up gt where lt name gt is the name of this viewing orientation lt Lefi gt specifies the coordinates of the viewing eye
48. Open Selecting Open from file menu pops up the dialog shown in Figure 4 3 The Raw files and Maxfilter output buttons change the file name filter to include names which end with raw fif or sss fif respectively to facilitate selection of original raw files or those processed with the Neuro mag Maxfilter software The options under Software gradient compensation allow selection of the compensation grade for the data These selections apply to the CTF data only The standard choices are No compensation and Third order gradient If other than No compensation is attempted for non CTF data an error will be issued The compensation selection affects the averages and noise covariance matrices subsequently computed The desired compensation takes effect independent of the compensation state of the data in the file i e already compensated data can be uncompensated and vice versa For more information on software gradient compensation please consult Section 9 2 4 The Keep the initial skip button controls how the initial segment of data not stored in the raw data file is handled During the MEG acquisition data are collected continuously but saving to the raw data file is controlled by the Record raw button Initial skip refers to the segment of data between the start of the recording and the first activation of Record raw If Keep initial skip is set this empty segment is taken into account in timing oth erwise time zero is set to the beginning
49. SSUBJECTS DIR and create the directory morph maps Load the inflated surface for subject morph as the morphing surfaces Try switching between the original and morphing surfaces More information about morphing is available in Section 7 9 and in Chapter 8 There is also a left hemisphere occipital patch file available for subject morph Load a righ hemifield visual response instead of the auditory one and investigate mapping of the current estimates on the patch 313 12 The sample data set 314 MSH MNE CHAPTER 13 Useful reading 13 1 General MEG reviews M H m l inen R Hari R Ilmoniemi J Knuutila and O V Lounasmaa Magnetoencephalography theory instrumentation and applications to noninvasive studies of the working human brain Reviews of Modern Physics vol 65 pp 413 497 1993 S Baillet J C Mosher and R M Leahy Electromagnetic Brain Map ping IEEE Signal Processing Magazine vol 18 pp 14 30 2001 M H m l inen and R Hari Magnetoencephalographic Characterization of Dynamic Brain Activation Basic Principles and Methods of Data Col lection and Source Analysis in Brain mapping the methods A W Toga and J C Mazziotta Eds Amsterdam Boston Academic Press 2002 13 2 Cortical surface reconstruction and morphing A M Dale B Fischl and M I Sereno Cortical surface based analysis I Segmentation and surface reconstruction Neuroimage vol 9 pp 179 94 1999 B Fi
50. T from the talair ach xfm file referred to in the MRI volume and the the fixed trans forms T_ and T will added to the output file For definition of the coordinate transformations see Section 5 2 talairach lt name gt Take the Talairach transform from this file instead of the one speci fied in mgh mgz files out lt name gt Specifies the output file which is a fif format MRI description file 9 9 Collecting coordinate transformations into one file The utility mne_collect_transforms collects coordinate transform infor mation from various sources and saves them into a single fif file The coordinate transformations used by MNE software are summarized in Figure 5 1 The output of mne_collect_transforms may include all trans forms referred to therein except for the sensor coordinate system transfor mations T y T T The command line options are version Show the program version and compilation date MSH MNE Data conversion 9 MSH MNE help List the command line options meas lt name gt Specifies a measurement data file which provides T A forward solution or an inverse operator file can also be specified as implied by Table 5 1 mri lt name gt Specifies an MRI description or a standalone coordinate transforma tion file produced by mne_analyze which provides T If the mgh option is not present mne_collect_transforms also tries to find T T T_ and T from this file mgh lt name gt An MR
51. Thereafter the variance of the source components tangential to the cortical surface are reduced by a factor defined by the loose option 3 A variable loose orientation constraint vLOC can be employed the loosevar option This is similar to LOC except that the value given with the loosevar option will be multiplied by 0 defined above Depth weighting The minimum norm estimates have a bias towards superficial currents This tendency can be alleviated by adjusting the source covariance matrix R to favor deeper source locations In the depth weighting scheme employed in MNE analyze the elements of R corresponding to the p source location are be scaled by a factor f T 7 T fi T 7 p Sip81ip T 82p82p 53p83p gt where g Pe and g p are the three colums of G corresponding to source location p and y is the order of the depth weighting specified with the weightexp option to mne_inverse_operator The maximal amount of depth weighting can be adjusted weightlimit option fMRI guided estimates The fMRI weighting in MNE software means that the source covariance matrix is modified to favor areas of significant fMRI activation For this purpose the MRI activation map is thresholded first at the value defined by the fmrithresh option to mne_do_inverse_operator Or mne_inverse_operator Thereafter the source covariance matrix values corresponding to the the sites under the threshold are multiplied by fotp set by th
52. User environment 000 es 325 B 2 Using Neuromag software 0c cee eee ees 325 Software OVErvieW 1 ee eee 325 Using MRIlab for coordinate system alignment 326 B 3 Mature software 000 ees 327 mne_compute_Mne eecegaeseeanes boeeaeedeedenne esse 327 viii MSH MNE Appendix C Installation and configuration C 1 C 2 C 3 C 4 System requirements Installation Download the software Installing from a compressed tar archive Installing from a Mac OSX disk image 5 Additional software Testing the performance of your OpenGL graphics Obtain FreeSurfer How to get started Appendix D Release notes MSH MNE D 1 Release notes for MNE software 2 4 0000uaes D 2 D 3 Manual General software changes 000 cece eens File conversion utilities mne_browse_raw mne_analyze mne_make_movie Averaging Release notes for MNE software 2 5 0000ceeues Manual mne_browse_raw mne_epochs2mat mne_analyze mne_ctfofiff mne_make_movie mne_surf2bem mne_forward_solution mne_inverse_operator mne_compute_raw_inverse 00 cece eee aes Time range settings mne_change_baselines New utilities mne_show_fiff mne_make_cor_set mne_compensate_data 0 eee eee mne_ins
53. addition it is possi ble to synthesize the digital trigger channel STI 014 from available ana log trigger channel data see the stim option below The synthesized trigger channel data value at sample k will be n 1 k A sH SY OT ped where t k are the thresholded from the input channel data d k 0 if d k St t k P 1 if d k gt t 219 9 Data conversion 220 The threshold value t can be adjusted with the stimthresh option see below mne_kit2fiff accepts the following command line options version Show the program version and compilation date help List the command line options elp lt filename gt The name of the file containing the locations of the fiducials and the HPI coils This option is mandatory hsp lt filename gt The name of the file containing the locations of the fiducials and additional points on the head surface This file is optional sns lt filename gt The name of file containing the sensor locations and orientations This option is mandatory hpi lt filename gt The name of a text file containing the locations of the HPI coils in the MEG device coordinate frame given in millimeters The order of the coils in this file does not have to be the same as that in the elp file This option is mandatory raw lt filename gt Specifies the name of the raw data file If this file is not specified the output fif file will only contain the measurement inf
54. alpha R G 3 E W Left hemi _ Transparent loa p3 i 04 Color W Right hemi I Transparent loa jos ps 04 Color W Inner skull Transparent i i i 04 Color W Scalp I Transparent pe joe os D4 Color J Digitizer data _ HP and landmarks only _ EEG electrodes o oi ps joa Color Helmet Transparent oo i i jos Color MEG sensors p3 ba is los Color W MEG field map EEG potential map J Activity estimates Figure 7 19 The viewer options window The viewer options window shown above contains three main sections to control the appearance of the viewer Selectors for various items to show Options for some of the items and 3 Control of the color and transparency of the items if applicable The color can be adjusted either by entering numeric values in the range 0 1 or with help of a color editor which appears from the Color but ton The transparency value has the same range as the other color com ponents zero indicating a fully transparent invisible surface and one a fully opaque one N e The available items are Left hemi The pial surface of the left hemisphere This surface can be made transparent Naturally this surface will only be visible if the scalp is made transparent Right hemi The pial surface of the right hemisphere MSH MNE 171 A Interactive analysis 172 Inner skull The inner skull surface This surface can be made transparent If parts of the pial surfa
55. around z axis using the cur rently specified rotation step This is useful for producing a 169 A Interactive analysis 170 sequence of images when automatic image saving is on see Section 7 8 7 Produces a image file which contains a snapshot of the currently displayed image For information on snapshot mode see Section 7 8 7 Stops the rotation invoked with the r key see above The left mouse button can be also used to inquire estimated magnetic field potential values on the helmet and head surfaces if the corresponding maps have been calculated and displayed In addition the mouse wheel or trackball can be used to rotate the image If a trackball is available e g with the Apple MightyMouse the image can be rotated up and down or left and right with the trackball With a mouse wheel the image will rotated up and down when the wheel is rotated Image rotation in the left right direction is achieved by holding down the shift key when rotating the wheel The shift key has the same effect on trackball operation Note The trackball and mouse wheel functionality is dependent on your X server settings On Mac OSX these settings are normally correct by default but on a LINUX system some adjustments to the X server settings maybe necessary Consult your system administrator or Google for details MSH MNE Interactive analysis A 7 10 2 Viewer options Viewer options Display components Item to show 1 Option 2
56. audvis ayve fif Proj Doriy a Delete Save W Left Auditory average N 55 Color W Right Aucitory average N 61 Color W Left visual gt average N 67 Color W Right visual gt average N 58 Color Al lh simuc fif Proj Corp Delete Save W Forward model gt average M 100 Color sample audvis ayve fif Proj o y Delete Save W Let Auditory average M 55 Color W Right Aucitory average N 61 Color W Left visual gt average N 67 Color Right visual gt average N 58 Color sample audvis ave fif Proj Dor eae Delete Save W Left Auditory average N 55 Color W Right Aucitory average N 61 Color Left visual gt average N 67 Color eer xr eee mv ate i Fi Figure 4 15 The dialog for managing available averages In the example of Figure 4 15 the first item is an average computed within mne_browse_raw the second one contains data loaded from a file with signal space projection data available the third one demonstrates multiple data sets loaded from a file with neither projection nor software gradient compensation available and the last one is a data set loaded from file with software gradient compensation data present Note that this is now a scrolled window and some of the loaded data may be below or above the current view area The Signal Space Projection SSP method The Signal Space Projection SSP is one approach to rejection of exter na
57. between values to be considered zero and non zero in the input file specified with the inmat option The default threshold is 10 out lt name gt Specifies output fif file to contain the derivation data The recom mended name of the derivation file has the format lt name gt deriv fif list lt name gt List the contents of a derivation file to standard output If this option is missing and out is specified the content of the output file will be listed once it is complete If neither List nor out is present and in or inmat is specified the interpreted con tents of the input file is listed Derivation file formats All lines in the input files starting with the pound sign are considered to be comments The format of a derivation in a arithmetic input file 1s lt name gt lt w gt lt name gt lt w gt lt name gt 283 1 Miscellaneous utilities 284 where lt name gt is the name of the derived channel name are the names of the channels comprising the derivation and w are their weights Note that spaces are necessary between the items Channel names containing spaces must be put in quotes For example EEG diff EEG 003 EEG 002 defines a channel EEG diff which is a difference between EEG 003 and EEG 002 Similarly EEG der 3 EEG 010 2 EEG 002 defines a channel which is three times EEG 010 minus two times EEG 002 The format of a
58. by mne_read_forward_solution see Table 10 30 Inverse operator decomposition data returned by mne_read_inverse_operator see Table 10 31 For more information on inverse operator decomposition see Section 6 2 For an example on how to compute inverse solution using this data see the sample routine mne_ex_compute_inverse wane ve seeon FIFFV_ MEG CH m This is a MEG channel FIFFV_REF MEG CH This a reference MEG channel located far away from the head FIFFV_EEF FIFFV EEFCH FIFFVEEFCH 2 This is an EEG channel Pavo n Tis MCG home FIFFV_ RESP CH 602 This channel contains respiration mon itor output FIFFV COORD UNKNOWN 0 Unknown coordinate frame FIFFV_COORD_DEVICE The MEG device coordinate frame FIFFV COORD_ISOTRAK 2 The Polhemus digitizer coordinate frame does not appear in data files FIFFV_COORD_HPI 3 HPI coil coordinate frame does not appear in data files FIFFV_COORD_HEAD 4 The MEG head coordinate frame Neu romag convention 262 Table 10 15 FIFF constants MSH MNE The Matlab toolbox 10 FIFFV FIFFV_COORD_MRI MRI 5 The MRI coordinate frame MRI coordinate frame FIFFV e a MRI_SLICE E coordinate frame of a single MRI slice FIFFV_COORD_MRI_DISPLAY The preferred coordinate frame for dis playing the MRIs used by MRIlab FIFFV COORD _DICOM_DEVICE The DICOM coordinate frame does not appear in files FIFFV_COORD_IMAGING_ DEVICE A generic imaging device coordinate frame does not appear
59. cess dade beseuseean see 4 4 295 Source waveform expressions 00 eee eee eee 295 11 14 Converting parcellation data into labels 298 Chapter 12 The sample data set 299 12l FUMOS 6405 rrr it See oe be PENE ETEDI EE E 299 12 2 OVGIVICW sea niaaa a Eia a a E 299 12 3 Seling UP cccucmetenesenkudecnstxcs meta EE 300 12 4 Contents of the data set 0 00 ccs 301 12 5 Setting up subject specific data 0 005 302 Structural MRIS anana aana ow oo ob a we ey was ww 9 302 Source Space as 4uaaee beau waa Oa oe eae eh ea eo 302 Boundary element models 0000 cece eee aes 303 12 6 Setting up a custom EEG layout 303 12 7 Previewing the data 0 c eee es 303 12 8 Off line averaging 0 00 cee ee 305 Using the averaging script interactively 305 MSH MNE vil Using the averaging script in batch mode 305 12 9 Viewing the off line average 0 000 eee eee eee 306 Loading the averages 40 00 cence es Heke ee eee ed aweaes 306 Inspecting the auditory data 2 0 0 eee eee ee 306 Inspecting the visual data 0 0 0 eee eee 307 12 10 Computing the noise covariance matrix 307 12 11 MEG MRI coordinate system alignment 308 Initial alignment ws lt cavecee ee ake eee eae heeeees seuss 308 Refining the coordinate transformation 309 Saving the transformation
60. component only settings in the MNE preferences dialog see Section 7 12 1 Timecourses at labels The labels provide means to interrogate timecourse information from ROIs The label files can be created in mne_analyze see Section 7 13 4 or in tksurfer which is part of the FreeSurfer software For mne_analyze left hemisphere and right hemisphere label files should be named lt name gt lh label and lt name gt rh label respectively Individual label files can be loaded from Labels Load label All label files in a directory can be loaded from Labels Load all labels Once labels are loaded the label list shown in Figure 7 22 appears Each time a new label is added to the list the names will be reordered to alphabetical order This list can be also brought up from Labels Show label list The list can be cleared from Labels Discard all labels Warning Because of the format of the label files mne_analyze can not certify that the label files loaded belong to the cortical surfaces of the present subject When a label is selected from the label list the corresponding timecourse appears The Keep button stores the timecourse to the timecourse man ager Section 7 13 3 MSH MNE Interactive analysis ia 000 X Labels Available labels AT Ih Calculate Average over vertices _j Maximum sample by sample _jL2 norm sample by sample _ Pick vertex with largest Lz norm over time ES ae Ka E Figure 7 22 The label
61. contain the orthogonal basis of the noise subspace corresponding to the signal space projection SSP operator P specified with one or more proj options so that P I UpU For more information on SSP see Section 4 16 With these definitions the map selections defined with the map option correspond to the following map 1 T Compute 2 8 A at each source space point Normalize the result so that the maximum values equals one map 2 T l l Compute g g at each source space point Normalize the result so that the maximum values equals one This is the amplitude of the signals produced by unit dipoles normal to the cortical surface MSH MNE Miscellaneous utilities 11 11 11 11 11 1 11 11 2 MSH MNE map 3 Compute Jg g gf at each source space point map 4 Compute Jg g gf at each source space point This could be called the radiality index map 5 Compute the subspace correlation between g and U subcorr g U g U pU 8_ g g This index equals zero if g is orthogonal to U and one if g lies in the subspace defined by U This map shows how close the field pattern of a dipole ori ented perpendicular to the cortex at each cortical location is to the subspace removed by the SSP map 6 Compute g Pg_ g g_ which is the fraction of the field pat tern of a dipole oriented perpendicular to the cortex at each cortical location remaining after applying the SSP a
62. conventions present in mne_do_forward_solution are lost However there are some special purpose options available in mne_forward_solution only Please refer to Section 3 11 for information on mne_do_forward_solution Command line options mne_forward_solution accepts the following command line options src lt name gt Source space name to use The name of the file must be specified exactly including the directory Typically the source space files reside in SUBJECTS_ DIR SUBJECT bem bem lt name gt Specifies the BEM to be used These files end with bem fif or bem sol fif and reside in SUBJECTS_DIR SUBJECT bem The former file contains only the BEM surface information while the latter files contain the geometry information precomputed with mne_prepare_bem_model see Section 5 7 If precomputed geome try is not available the linear collocation solution will be computed by mne_forward_solution origin lt x mm gt lt x mm gt lt z mm gt Indicates that the sphere model should be used in the forward calcu lations The origin is specified in MEG head coordinates unless the mricoord option is present The MEG sphere model solution computed using the analytical Sarvas formula For EEG an approx imative solution described in 113 a The forward solution 114 eegmodels lt name gt This option is significant only if the sphere model is used and EEG channels are present The specified file contains specifications
63. convert it to fif format for use with mne_browse_raw see Section 11 5 BEM mesh generation All information concerning BEM mesh generation has been moved to Appendix A Utilities for BEM mesh generation using FLASH images have been added see Section A 2 Matlab toolbox The MNE Matlab toolbox has been significantly enhanced New features include e Basic routines for reading and writing fif files e High level functions to read and write evoked response fif data e High level functions to read raw data e High level routines to read source space information covariance matri ces forward solutions and inverse operator decompositions directly from fif files MSH MNE Release notes D MSH MNE D 3 D 3 1 D 3 2 D 3 3 The Matlab toolbox is documented in Chapter 10 The mne_div_w utility has been removed because it is now easy to per form its function and much more using the Matlab Toolbox Release notes for MNE software 2 6 Manual The changes described below briefly are documented in the relevant sec tions of the manual Change bars are employed to indicate changes with respect to manual version 2 5 Chapter 5 now contains a comprehensive discussion of the various coordinate systems used in MEG EEG data Command line options All compiled C programs now check that the command line does not con tain any unknown options Consequently scripts that have inadvertently specified some options which are invalid wi
64. cov f1f If this file contains a projection operator which will automatically attached to the noise covariance matrix by mne_browse_raw and mne_process_raw no proj option is necessary because mne_inverse_operator will automatically include the projectors from the noise covariance matrix file megreg lt value gt Regularize the MEG part of the noise covariance matrix by this amount Suitable values are in the range 0 05 0 2 For details see Section 6 2 4 eegreg lt value gt Like megreg but applies to the EEG channels diagnoise Omit the off diagonal terms of the noise covariance matrix This option is irrelevant to most users fmri lt name gt With help of this w file an a priori weighting can be applied to the source covariance matrix The source of the weighting is usually fMRI but may be also some other data provided that the weighting can be expressed as a scalar value on the cortical surface stored in a w file It is recommended that this w file is appropriately smoothed see Section 8 3 in mne_analyze tksurfer or with mne_smooth_w to contain nonzero values at all vertices of the triangular tessellation of the cortical surface The name of the file given is used as a stem of the w files The actual files should be called lt name gt 1lh pri and lt name gt rh pri for the left and right hemisphere weight files respectively The application of the weighting is discussed in Section 6 2 11 MSH MNE 37 al
65. current estimates are visualized on inflated or folded cortical surfaces There are two visualization displays the surface display which is always visible and the 3D viewer which is invoked from the Windows Show viewer menu Selection see Section 7 10 A total of eight surfaces or patches can be assigned to the surface display L The left and right hemisphere cortical surfaces for the subject whose data you are analyzing These surfaces can be the inflated white mat ter or pial surfaces They are loaded through the File Load surface menu selection The left and right hemisphere cortical surfaces of another subject or an alternative representation of the cortical surface of the actual subject For example you can switch between the inflated and folded pial or white matter cortical surfaces very easily These surfaces are loaded from the File Load morphing surface menu selection Left and right hemisphere curved or flat cortical patches for the subject you are analyzing This patch is loaded from the File Load surface MSH MNE Interactive analysis 7 patch menu selection The full cortical surfaces must be loaded first before loading the patches 4 Patches for an another subject or another pair of patches for the same subject through the File Load morphing surface patch menu selec tion Again the full cortical surfaces must have been loaded first 7 8 1 The surface selection dialog When File Load su
66. different electrical conductivities are tessellated with suitable surface elements Our BEM software employs triangular tessellations Therefore prerequisites for BEM calculations are the segmentation of the MRI data and the triangula tion of the relevant surfaces For MEG computations a reasonably accurate solution can be obtained by using a single compartment BEM assuming the shape of the intracra nial volume For EEG the standard model contains the intracranial space the skull and the scalp At present no bulletproof method exists for creating the triangulations Feasible approaches are described in Appendix A Setting up the triangulation files The segmentation algorithms described in Appendix A produce either FreeSurfer surfaces or triangulation data in text Before proceeding to the creation of the boundary element model standard files or symbolic links created with the ln s command have to be present in the subject s bem directory If you are employing ASCII triangle files the standard file names are inner_skull tri Contains the inner skull triangulation outer_skull tri Contains the outer skull triangulation outer_skin tri Contains the head surface triangulation The corresponding names for FreeSurfer surfaces are inner_skull surf Contains the inner skull triangulation outer_skull surf Contains the outer skull triangulation MSH MNE The Cookbook al MSH MNE outer_skin surf Contains the hea
67. dipole remaining Transforming locations Purpose mne_transform_points applies the coordinate transformation relating the MEG head coordinates and the MRI coordinates to a set of locations listed in a text file Command line options mne_transform_points accepts the following command line options version Show the program version and compilation date help List the command line options In lt name gt Specifies the input file The file must contain three numbers on each line which are the x y and z coordinates of point in space By default the input is in millimeters ISO lt name gt Specifies a name of a fif file containing Isotrak data If this option is present file will be used as the input instead of the text file specified with the in option 291 1 Miscellaneous utilities 292 trans lt name gt Specifies the name of a fif file containing the coordinate transforma tion between the MEG head coordinates and MRI coordinates If this file is not present the transformation will be replaced by a unit transform out lt name gt Specifies the output file This file has the same format as the input file hpts Output the data in the head points hpts format accepted by tkmedit In this format the coordinates are preceded by a point cate gory hpi cardinal or fiducial eeg extra and a sequence number see Section 9 3 1 meters The coordinates are listed in meters rather than millimeters
68. display Additional browsing functionality will be discussed n In addition if the strip chart display has the keyboard focus you can scroll back and forth with the page up and page down keys Selection of time points When you click on the data with the left button a vertical marker appears If Show segments in full view and or Show segments in sample view is active in the scales dialog see Section 4 5 2 a dis play of an epoch of data specified in the scales dialog will appear For more information on full view see Section 4 12 Multiple time points can be selected by holding the control key down when click ing If multiple time points are selected several samples will be shown in the sample and or full view aligned at the picked time point The tool bar offers functions to operate on the selected time points see Section 4 11 Range selection Range selection If you drag on the signals with the left mouse but ton and the shift key down a range of times will be selected and dis played in the sample and or full view Note All previous selections are cleared by this operation Saving a copy of the display The right mouse button invokes a popup menu which allows saving of the display in various formats Best quality is achieved with the MSH MNE 69 4 Processing raw data 70 4 9 1 Illustrator format This format has the benefit that it is object ori ented and can be edited in Adobe Illustrator Drag and drop Graphic
69. identical to that of the Neuromag MEG EEG head coordinate system However in 4 D Neuroimaging and CTF MEG systems the head coordinate frame definition is different The origin of the coordinate system is at the midpoint of the left and right auricular points The x axis passes through the nasion and the origin with positive direction to the front The y axis is perpendicular to the x axis on the and lies in the plane defined by the three fiducial landmarks positive direction from right to left The z axis is normal to the plane of the land marks pointing up Note that in this convention the auricular points are not necessarily located on y coordinate axis The file conversion utilities see Section 9 2 take care of these idiosyncrasies and convert all coordi nate information to the MNE software head coordinate frame 97 Ee The forward solution 98 5 4 Creating a surface based source space The fif format source space files containing the dipole locations and orien tations are created with the utility mne_make_source_space This utility is usually invoked by the convenience script mne_setup_source_space see Section 3 5 The command line options are version Show the program version and compilation date help List the command line options subject lt name gt Name of the subject in SUBJECTS_DIR In the absense of this option the SUBJECT environment variable will be consulted If it is not defined mne_setup_source_s
70. in fif format These binary event files can be read and written with the mne_read_events and mne_write_events functions in the MNE Matlab toolbox see Chapter 10 For more information on events see Section 4 10 Load derivations This menu choice allows loading of channel derivation data files created with the mne_make_derivations utility see Section 11 5 or using the interactive derivations editor in mne_browse_raw see Section 4 5 4 Most common use of derivations is to calculate differences between EEG chan nels i e bipolar EEG data Since any number of channels can be included in a derivation with arbitrary weights other applications are possible as well Before a derivation is accepted to use the following criteria have to be met MSH MNE Processing raw data 4 MSH MNE 4 4 13 4 4 14 4 4 15 1 All channels to be combined into a single derivation must have identi cal units of measure 2 All channels in a single derivation have to be of the same kind e g MEG channels or EEG channels 3 All channels specified in a derivation have to be present in the currently loaded data set Multiple derivation data files can be loaded by specifying the Keep previ ous derivations option in the dialog that specifies the derivation file to be loaded After a derivation file has been successfully loaded a list of avail able derivations will be shown in a message dialog Each of the derived channels has a name specified when
71. in step 6 bad for this viewing session by clicking on their channel names on the left You can save the bad channel selection to the file from File Apply bad channels Bad channel marking can be removed by clicking on their channel names again and selecting File Apply bad channels Alternatively you can use the utility mne_mark_bad_channels to set a bad channel selection see Section 11 4 1 Switch the projections back on and change filter to a 40 Hz lowpass Compute a preliminary average for the left ear auditory stimulus a Open the averaging preferences dialog Adjust Averaging prefer ences b Set the time scale to 100 300 ms c Click on the text next to Average in the main window and press return After a while a topographical display appears with the aver aged responses Notice that the bad channels are not displayed d Change to different layouts from Adjust Full view layout Inspect both the MEG and EEG waveforms Compute a preliminary average for the right ear auditory stimulus a Open the averaging preferences b Click on the Trace color button and change the trace color to something different from the default yellow c Change the text next to Average to 2 and press return Average to the right ear tones will be computed Compare the to sets of aver ages and verify that all channels show reasonable data Go to Windows Manage averages and delete the preliminary aver ages just computed
72. is not exceed anon Do not include any subject information in the output files created with the save option decim lt number gt The data are decimated by this factor before saving to the file speci fied with the save option For decimation to succeed the data must be lowpass filtered to less than third of the sampling frequency effective after decimation 47 4 Processing raw data 4 3 The user interface 009 X Browse and process File Adjust Process Windows lt Remove dc Keep dc Jump to In e Picked to ooo Forget 1000 Average R 3 No data loaded Ready to go Figure 4 1 The user interface of mne_browse_raw The mne_browse_raw user interface contains the following areas 1 The menu bar 2 The data display area 3 Viewing and averaging tools 4 Message line The viewing and averaging tools allow quick browsing of the raw data with triggers adding new triggers and averaging on a single trigger 48 MSH MNE Processing raw data 4 4 4 The File menu MSH MNE 4 4 1 Open Alta Save Alt s Open evoked Change working directory Read projection save projection Apply bad channels Load events text save events text save events fif Load derivations save derivations Load channel selections save channel selections Quit Alt G Figure 4 2 The contents of the File menu The File menu pane is shown in Figure 4 2
73. lt data type gt f 1if and rh lt data type gt 1if respectively lt data type gt equals mne for expected current data and spm for dSPM data For raw data _raw fif is employed instead of fif The output files are stored in the same directory as the label files labelselout Produces additional label files for each label processed containing only those vertices within the input label which correspond to avail able source space vertices in the inverse operator These files have the same name as the original label except that 1h and rh are replaced by sel 1h and sel rh respectively align_z Instructs the program to try to align the waveform signs within the label For more information see Section 6 6 2 This flag will not 142 MSH MNE The current estimates E MSH MNE have any effect 1f the inverse operator has been computed with the strict orientation constraint active labeldir lt directory gt All previous label options will be ignored when this option is encountered For each label in the directory the output file defined with the out option will contain a summarizing waveform which is the average of the waveforms in the vertices of the label The labeldir option implies align z and picknormal comp options orignames This option is used with the Labeldir option above With this option the output file channel names will be the names of the label files truncated to 15 character
74. matrix This field may be empty for a diagonal covariance matrix double dim dim The eigenvectors of the covariance matrix Table 10 29 The cov structure Field Datatype Data type T e source_ori int32 Has sieccul on been computed r eee solution been computed for the current com ponent normal to the cortex only 1 or all three source orientations 2 coord_frame int32 Coordinate frame in which the locations and orienta tions are e sol_grad named matrix The derivatives of the forward solution with respect to the dipole location coordinates see Section 5 9 6 This field is present only 1f the forward solution was computed with the grad option see Section 5 9 2 mri_head_t trans Transformation from the MRI coordinate frame to the Neuromag head coordinate frame O E of the source spaces SCSC double nsource 3 The source locations source_nn double 3 The source orientations Number of rows is either nsource fixed source orientations or 3 nsource all source orientations Table 10 30 The fwd structure 272 MSH MNE The Matlab toolbox methods int32 Has the solution been computed using MEG data 1 EEG data 2 or both 3 source_ori int32 Has the solution been computed for the current component normal to the cortex only 1 or all three source orientations 2 coord_frame int32 Coordinate frame in which the locations and orien tations are expressed source_nn double 3 The source orientations
75. mne_analyze the SUBJECTS DIR environment variable has to be set Note Strictly speaking trigger mask value zero would mean that all trig ger inputs are ignored However for convenience setting the mask to zero or not setting it at all has the same effect as OXFFFFFFFF i e all bits set Tip The digital trigger channel can also be set with the MNE_ENV_TRIGGER_ CH environment variable Underscores in the variable value will not be replaced with spaces by mne_analyze Using the digtrig option supersedes the MNE_ENV_TRIGGER_CH environ ment variable Tip The digital trigger channel mask can also be set with the MNE_TRIGGER_CH_MASK_ environment variable Using the digtrigmask option supersedes the MNE_ TRIGGER _CH_MASK environment variable 146 MSH MNE Interactive analysis A 7 3 The main window X This should be quite convenient File Adjust Windows Labels 1 Help Sample channel N A m One hemisphere Data 2 SNR N A 3 ut MNE amplitude not computed 4 Adjust View T Output E a ajale te e al yee im nv time ms Ready to go D k Figure 7 1 The main window of mne_analyze The main window of mne_analyze shown in Figure 7 1 has the following components The menu bar Display area for a sample response Display of the estimated SNR see Section 7 12 2 Display of a source wavefo
76. mne_compute_mne have been removed mne_compute_mne can now process only the entire averaged epoch 330 MSH MNE appenpix c Installation and configuration MSH MNE C 1 C 2 C 2 1 C 2 2 System requirements The MNE software runs on Mac OSX and LINUX operating systems The hardware and software requirements are 1 Mac OSX version 10 5 Leopard or later 2 LINUX kernel 2 6 9 or later 3 On both LINUX and Mac OSX 32 bit and 64 bit Intel platforms are supported PowerPC version on Mac OSX can be provided upon request 4 At least 2 GB of memory 4 GB or more recommended 5 Disk space required for the MNE software 80 MB 6 Additional open source software on Mac OSX see Section C 2 4 Installation The MNE software is distributed as a compressed tar archive Mac OSX and LINUX or a Mac OSX disk image dmg Download the software Download the software package of interest The file names follow the con vention MNE lt version gt lt rev gt lt Operating system gt lt Processor gt lt ext gt The present version number is 2 7 0 The lt rev gt field is the SVN revision number at the time this package was created The lt Operating system gt field is either Linux or MacOSX The lt processor gt field is either 1386 or x86_64 The lt ext gt field is gz for compressed tar archive files and dmg for Mac OSX disk images Installing from a compressed tar archive Go to the directory where you want t
77. of the EEG sphere model layer structures as detailed in Section 5 9 4 If this option is absent the file SHOME mne EEG models will be consulted if it exists eegmodel lt model name gt Specifies the name of the sphere model to be used for EEG If this option is missing the model Default will be employed see Section 5 9 4 eegrad lt radius mm gt Specifies the radius of the outermost surface scalp of the EEG sphere model see Section 5 9 4 The default value is 90 mm eegscalp Scale the EEG electrode locations to the surface of the outermost sphere when using the sphere model accurate Use accurate MEG sensor coil descriptions This is the recom mended choice More information fixed Compute the solution for sources normal to the cortical mantle only This option should be used only for surface based and discrete source spaces all Compute the forward solution for all vertices on the source space label lt name gt Compute the solution only for points within the specified label Multiple labels can be present The label files should end with lh label or rh label for left and right hemisphere label files respectively If all flag is present all surface points falling within the labels are included Otherwise only decimated points with in the label are selected mindist lt dist mm gt Omit source space points closer than this value to the inner skull surface Any source space points outside the i
78. of the data stored to disk 49 4 Processing raw data 50 When a raw data file is opened the digital trigger channel is scanned for events For large files this may take a while Note After scanning the trigger channel for events mne_browse_raw and mne_process_raw produce a fif file containing the event information This file will be called lt raw data file name without fif extension gt eve fif If the same raw data file is opened again this file will be consulted for event information thus making it unnecessary to scan through the file for trigger line events Tip You can produce the fif event file by running mne_process_raw as follows mme process raw raw lt raw data file gt The fif format event files can be read and written with the mne_read_events and mne_write_events functions in the MNE Matlab toolbox see Chapter 10 X Open a raw data file Filter idata sample dataMEG sample _raw fit Directories Files sample audvis_raw fit test_decim_rawfif i j m e j List Raw files Manxtilter output files software gradient compensation No compensation _ First order gradient _ Second order gradient _ Third order gradient _ 40 compensation 1 J Keep the initial skip selection sers mnshidata sample dataMEG sampled Figure 4 3 The Open dialog 4 4 2 Open evoked This menu item brings up a standard file selection dialog to load evoked r
79. often used to denotes menu selections For example File Quit stands for the Quit button in the File menu All software modules employ the double dash option convention i e the option names are preceded by two dashes Most of the programs have two common options to obtain general infor mation help Prints concise usage information version Prints the program module name version number and compilation date User environment The system dependent location of the MNE Software will be here referred to by the environment variable MNE_ROOT There are two scripts for set ting up user environment so that the software can be used conveniently SMNE ROOT mne setup mne mne setup sh and MSH MNE Overview E SMNE ROOT mne setup mne mne setup compatible with the POSIX and csh tcsh shells respectively Since the scripts set environment variables they should be sourced to the present shell You can find which type of a shell you are using by saying echo SSHELL If the output indicates a POSIX shell bash or sh you should issue the three commands export MNE ROOT lt MNE gt export MATLAB ROOT lt Matlab gt SMNE ROOT bin mne setup sh with lt MNE gt replaced by the directory where you have installed the MNE software and lt Matlab gt is the directory where Matlab is installed If you do not have Matlab leave MATLAB_ROOT undefined If Matlab is not available the utilities mne_convert_mne_data mne_epo
80. on trigger channel STI 014 This can be fixed by running mne_fix_stim14 on the raw data file before using mne_browse_raw or mne_process_raw The bug has been fixed on Nov 10 2005 4 13 2 Common parameters The average definition starts with the common parameters They include outfile lt name gt The name of the file where the averages are to be stored In interac tive mode this can be omitted The resulting average structure can be viewed and stored from the Manage averages window eventfile lt name gt Optional file to contain event specifications If this file is present the trigger events in the raw data file are ignored and this file is con sulted instead The event file format is recognized from the file name if it ends with fif the file is assumed to be in fif format otherwise a text file is expected The text event file format is described in Section 4 10 5 T 4 Processing raw data 78 logfile lt name gt This optional file will contain detailed information about the averag ing process In the interactive mode the log information can be viewed from the Manage averages window eradReject lt value T m gt Rejection limit for MEG gradiometer channels If the peak to peak amplitude within the extracted epoch exceeds this value on any of the gradiometer channels the epoch will be omitted from the aver age magReject lt value T gt Rejection limit for MEG magnetometer and axial gradiometer chan nels
81. pp 47 62 2002 F H Lin J W Belliveau A M Dale and M S Hamalainen Distrib uted current estimates using cortical orientation constraints Hum Brain Mapp vol 27 pp 1 13 2006 T F Oostendorp J Delbeke and D F Stegeman The conductivity of the human skull results of in vivo and in vitro measurements IEEE Trans Biomed Eng vol 47 pp 1487 92 Nov 2000 S I Gon alves J C de Munck J P Verbunt F Bijma R M Heethaar and F Lopes da Silva In vivo measurement of the brain and skull resis tivities using an EIT based method and realistic models for the head IEEE Trans Biomed Eng vol 50 pp 754 67 2003 S Lew C H Wolters A Anwander S Makeig and R S MacLeod Improved EEG source analysis using low resolution conductivity estima tion in a four compartment finite element head model Hum Brain Mapp vol 30 pp 2862 78 2009 13 6 fMRI weighted estimates A M Dale A K Liu B R Fischl R L Buckner J W Belliveau J D Lewine and E Halgren Dynamic statistical parametric mapping com bining MRI and MEG for high resolution imaging of cortical activity Neuron vol 26 pp 55 67 2000 A K Liu J W Belliveau and A M Dale Spatiotemporal imaging of human brain activity using functional MRI constrained magnetoencepha lography data Monte Carlo simulations Proc Natl Acad Sci U S A vol 95 pp 8945 50 1998 F H Lin T Witzel M S Hamalainen A M Dale J
82. procedure afterwards The drawback of this approach is that the spacing between source locations in the morph subject is not going to be as uniform as it would be without morphing Spacing lt spacing mm gt Specifies the grid spacing for the source space in mm If not set a default spacing of 7 mm is used Either the default or a 5 mm spac ing is recommended ico lt number gt Instead of using the traditional method for cortical surface decima tion it is possible to create the source space using the topology of a recursively subdivided icosahedron lt number gt gt 0 or an octahe dron lt number gt lt 0 This method uses the cortical surface inflated to a sphere as a tool to find the appropriate vertices for the source space The benefit of the ico option is that the source space will have triangulation information for the decimated vertices included which future versions of MNE software may be able to utilize The number of triangles increases by a factor of four in each subdivi sion starting from 20 triangles in an icosahedron and 8 triangles in an octahedron Since the number of vertices on a closed surface is Avot Ny 4 72 the number of vertices in the kth subdivision of an icosahedron and an octahedron are 10 4 2 and 4 2 i respectively The recommended values for lt number gt and the corre sponding number of source space locations are listed in Table 3 1 surface lt name gt Name of the sur
83. saying help lt routine name gt in Matlab 274 MSH MNE cHapter 11 Miscellaneous utilities MSH MNE 11 1 Overview This Chapter describes various utility programs included with the MNE software Each utility documentation consists of a brief description of the purpose followed by the specification of command line options 11 2 Finding software versions The utility mne_list_versions lists version numbers and compilation dates of all software modules that provide this information This administration utility is located in SMNE ROOT bin admin The output from mne_list_versions or output of individual modules with version option is useful when bugs are reported to the developers of MNE soft ware 11 3 Listing contents of a fif file Using the utility mne_show_fiff it is possible to display information about the contents of a fif file to the standard output The command line options for mne_show_fiff are version Show the program version and compilation date help List the command line options In lt name gt Specifies the fif file whose contents will be listed verbose Produce a verbose output The data of most tags is included in the output This excludes matrices and vectors Only the first 80 charac ters of strings are listed unless the long option is present 275 1 Miscellaneous utilities 2 6 blocks Only list the blocks the tree structure of the file The tags within each block are not list
84. see Chapter 10 These functions require running the script mne_setup_mri which requires that the subject is set with the subject option or by the SUBJECT environment variable The script processes one or more MRI data sets from SSUBJECTS DIR SSUBJECT mri by default they are T1 and brain This default can be changed by specifying the sets by one or more mri options MSH MNE The Cookbook a MSH MNE The script creates the directories mri lt name gt neuromag slices and mri lt name gt neuromag sets If the the input data set is in COR format mne_setup_mri makes symbolic links from the COR files in the directory mri lt name gt into mri lt name gt neuromag slices and creates a corresponding fif file COR fif in mri lt name gt neuromag sets This description file contains references to the actual MRI Slices If the input MRI data are stored in the newer mgz format the file created in the mri lt name gt neuromag sets directory will include the MRI pixel data as well If available the coordinate transformations to allow conversion between the MRI surface RAS coordinates and MNI and FreeSurfer Talairach coordinates are copied to the MRI description file mne_setup_mri invokes mne_make_cor_set described in Section 9 8 to convert the data For example mne setup mri subject duck donald mri Tl This command processes the MRI data set T1 for subject duck_donald Tip If the SUBJECT environment variable is set i
85. sparse blurring matrix a a On each row jof the matrix SP there are NY D nonzero entries whose values equal 1 M7 Here NPD is the number of immediate neigh bors of vertex j which had non zero values at iteration step p 1 Matrix SV thus assigns the average of the non zero neighbors as the new value for vertex 7 One important feature of this procedure is that it tends to pre serve the amplitudes while blurring the surface image _ 0 Once the indices non zero vertices in x and the topology of the triangu lation are fixed the matrices SY are fixed and independent of the data Therefore it would be in principle possible to construct a composite blur ring matrix N s TTS p l MSH MNE Morphing and averaging 8 MSH MNE However it turns out to be A more effective to do blurring with an iteration The above formula for S gt also shows that the smudg ing smoothing operation is linear 8 4 Precomputing the morphing maps The utility mne_make_morph_maps was created to assist mne_analyze and mne_make_movie in morphing Since the morphing maps described above take a while to compute it is beneficial to construct all necessary maps in advance before using mne_make_movie The precomputed mor phing maps are located in SUBJECTS DIR morph maps mne_make_morph_maps creates this directory automatically 1f it does not exist If this directory exists when mne_analyze or mne_make_movie i
86. specifies a time range for raw data covariance matrix estimation and the file to hold the result If a covariance matrix 1s computed in this way the rejection parameters specified in averaging preferences are in effect For description of the rejection parameters see Section 4 5 9 The time range can be also selected interactively from the main raw data display by doing a range selection with shift left button drag Creating a new SSP operator The Create a new SSP operator menu choice computes a new SSP oper ator as discussed in Section 4 16 2 65 4 Processing raw data 66 Compute a new SSP operator Start time 3 i End time s 1000 Event to use 0 for continuous B Compute Cancel Help Figure 4 11 Time range specification for SSP operator calculation When Create a new SSP operator selected a window shown in Figure 4 11 1s popped up It allows the specification of a time range to be employed in the calculation of a raw data covariance matrix The time range can be also selected interactively from the main raw data display by doing a range selection with shift left button drag Normally you should use empty room data for this computation For the estimation of the cova riance matrix any existing projection will be temporarily switched off Remember to inspect your data for bad channels and select an appropriate filter setting before creating a new SSP operator The artifact rejection parameters specifi
87. starting point of the epoch with respect to the event of interest tmax lt time ms gt The endpoint of the epoch with respect to the event of interest sel lt name gt Specifies a text file which contains the names of the channels to include in the output file one channel name per line If the inv option is specified sel is ignored If neither inv nor sel is present all MEG and EEG channels are included The digital trig ger channel can be included with the includetrig option described below InvV lt name gt Specifies an inverse operator which will be employed in two ways First the channels included to output will be those included in the inverse operator Second any signal space projection operator present in the inverse operator file will be applied to the data This option cancels the effect of sel and proj options MSH MNE 247 9 Data conversion 248 digtrig lt name gt Name of the composite digital trigger channel The default value is STI 014 Underscores in the channel name will be replaced by spaces digtrigmask lt number gt Mask to be applied to the trigger channel values before considering them This option is useful if one wants to set some bits in a don t care state For example some finger response pads keep the trigger lines high if not in use i e a finger is not in place Yet it is conve nient to keep these devices permanently connected to the acquisition system
88. steps are taken MSH MNE Morphing and averaging 8 As the labels are morphed a directory with the name of the subject speci fied with the to option is created under the directory specified with labeldir to hold the morphed labels 8 6 Averaging 8 6 1 Overview As illustrated in Figure 8 1 cross subject averaging involves three straightforward steps 1 Use mne_make_movie to create stc files morphed to a single subject This requires the use of the morph option see Section 6 5 5 The resulting files will have identical selections of vertices on the cortical surface of the subject used in averaging This step can be speeded up by precomputing the morphing maps employed in the process see Section 8 4 2 Employ mne_average_estimates or a Matlab script to read the data from the stc files and to produce an output stc file containing the aver aged data The MNE Matlab toolbox routines for reading and writing stc files are documented in Chapter 10 3 Use mne_analyze or mne_make_movie to visualize the result or use the stc files from the previous step in your own Matlab routines in further processing Measurement data Surface files Inverse operators Surface files Morphing maps optional mne_make_morph_maps 8 4 Morphed stc files mne_make_movie 6 5 Averaged stc files mne_average_estimates 8 6 Quicktime movies snapshots w files mne_make_movie 6 7 mne_analyze 7 Figure 8 1 Work
89. subject gt lt spacing gt lh pnt and lt subject gt lt spacing gt rh pnt containing the source space points in MRIlab compatible ascii format 3 lt subject gt lt spacing gt lh dip and lt subject gt lt spacing gt rh dip containing the source space points in MRIlab compatible ascii format These files contain dipoles i e both source space points and cortex normal directions 4 If cortical patch statistics is requested another source space file called lt subject gt lt spacing gt p src f 1if will be created Note lt spacing gt will be the suggested source spacing in millimeters if the Spacing option is used For source spaces based on kth subdivi sion of an icosahedron lt spacing gt will be replaced by ico k or oct k respectively Tip After the geometry is set up it is possible to check that the source Space points are located on the cortical surface This can be easily done with by loading the COR fif file from mri T1 neuromag sets into MRIlab and by subsequently overlaying the corresponding pnt or dip files using mport Strings or Import Dipoles from the File menu respectively 23 al The Cookbook 24 Tip If the SUBJECT environment variable is set correctly it is usually sufficient to run mne setup source space without any options 3 6 Creating the BEM model meshes 3 6 1 Calculation of the forward solution using the boundary element model BEM requires that the surfaces separating regions of
90. system dependent For example in a well shielded quiet environment no planar gradiometer projections are usually needed projnmag lt number gt Number of SSP components to include for magnetometers axial gradiometers default 8 This value is system dependent For example in a well shielded quiet environment 3 4 components are need while in a noisy environment with light shielding even more than 8 components may be necessary projgradrej lt value fT cm gt Rejection limit for planar gradiometers in the estimation of the covariance matrix frfixom which the new SSP operator is derived The default value is 2000 fT cm Again this value is system depen dent projmagrej lt value fT gt Rejection limit for planar gradiometers in the estimation of the covariance matrix from which the new SSP operator is derived The default value is 3000 fT Again this value is system dependent Saveprojtag lt tag gt This option defines the names of files to hold the SSP operator If this option is present the makeproj option is implied The SSP operator file name is formed by removing the trailing fif or _raw fif from the raw data file name by appending lt tag gt fif to this stem Recommended value for lt tag gt is proj Saveprojaug Specify this option if you want to use the projection operator file output in the Elekta Neuromag Signal processor graph software 45 4 Processing raw data eventsout lt name gt
91. the elements of the rotation matrix relating the two coordinate systems The coordinate transformations are present in different files produced by FreeSurfer and MNE as summarized in Table 5 1 The fixed transformations T_ and T are 0 99 0 0 0 r 9 0 9688 0 042 0 0 0 0485 0 839 0 0 0 0 and 95 a The forward solution 0 99 0 0 0 r 0 0 9688 0 046 0 QO 0 0485 0 9189 0 0 0 0 Note This section does not discuss the transformation between the MRI voxel indices and the different MRI coordinates However it is important to note that in FreeSurfer MNE as well as in Neuromag software an inte ger voxel coordinate corresponds to the location of the center of a voxel Detailed information on the FreeSurfer MRI systems can be found at https surfer nmr mgh harvard edu fsw1ki CoordinateSystems m Notpresent present Measurement E data PE files Forward solution files fwd fif Inverse operator files inv fif Not present Channel information in files con taining T Not present MRI description files Separate coordinate transformation files saved from mne_analyze Forward solution files Inverse operator files mri mgz files MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format mri transforms talairach xfm MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format Hardcoded in software MRI description files saved with mne_ma
92. the number of time points n em 18 the number of comment lines lras ty indicate the times in milliseconds p is a vertex number Xn Vn Zp l are the coordinates of vertex p in millimeters and vi Lo are the values at vertex p Items in brackets are only included if Include coordinates 1s active In the time by time output format the data portion of the file is transposed 7 13 4 Creating new label files It is easy to create new label files in mne_analyze For this purpose an inflated surface should be visible in the main display Follow these steps 1 Clear all previously selected vertices either by choosing Labels Clear marked vertices or do a right button click on the surface display with the shift key down 2 Mark vertices on the surface with right button click or by right button drag The vertices should be defined in the desired order on the new label outline The outline will follow the shortest path along the sur face The shortest path will be calculated along the white matter sur face Note that sometimes the shortest paths appear to be un intuitive on the inflated surface 3 Do aright button click with control key down inside the label The out line will be completed and shown as a yellow line The inside of the MSH MNE 183 Ea Interactive analysis 184 label will be filled and shown in green A file selection box will appear to save the label Enter the stem of the file name here The file name will be augment
93. the other two landmark points Nasion and LAP Left Auricular Point 9 Press Align using fiducials Notice that the coordinate transformation changes from a unit transformation no rotation no origin translation to a one determined by the identified landmark locations The rotation matrix upper left 3 x 3 part of the transformation should have positive N MSH MNE The sample data set 12 MSH MNE values close to one on the diagonal Three is a significant rotation around the x axis as indicated by elements 3 2 and 2 3 of the rota tion matrix The x and y values of the translation should be small and the z value should be negative around 50 mm An example of an 1ni tial coordinate transformation is shown in Figure 12 1 10 Make the Digitzer data again visible from the options of the viewer window Note that the points are now much coloser to the scalp sur face Current coordinate transformation head gt WIRI 0 997093 0 057963 0 048446 2 76 mm 0 037656 0 999130 0 341481 7a mm 0 066230 0 336636 0 936563 48 54 mm O O00000 O 000000 0 000000 1 00 Fiducial xMRI mm yMRI mm zMRI mm LAP EZ jas baa Nasion Bs a7 H28 RAP p28 Ho isa Figure 12 1 Example of an initial coordinate alignment 12 11 2 Refining the coordinate transformation Before proceeding to the refinement procedure it is useful to remove out lier digitizer points When you rotate the image in the viewer window you will notice that t
94. the pound sign are considered to be comments smooth lt nstep gt Number of smoothsteps to take when producing the output frames Depending on the source space decimation an appropriate number is 4 7 Smoothing does not have any effect for the original brain if stc files are produced However if morphing is selected smoothing is mandatory even with stc output For details of the smoothing pro cedure see Section 8 3 nocomments Do not include the comments in the image output files or movies noscalebar Do not include the scalebar in the image output files or movies 6 5 6 Thresholding fthresh lt value gt Specifies the threshold for the displayed colormaps At the thresh old the overlayed color will be equal to the background surface color For currents the value will be multiplied byl The default value is 8 fmid lt value gt Specifies the midpoint for the displayed colormaps At this value the overlayed color will be read positive values or blue negative values For currents the value will be multiplied byl The default value is 15 fmax lt value gt Specifies the maximum point for the displayed colormaps At this value the overlayed color will bright yellow positive values or light blue negative values For currents the value will be multi plied byl The default value is 20 fslope lt value gt Included for backwards compatibility If this option is specified an
95. the values of various FIFF constants defined by fiff_define_constants m The documented structures are tag Contains one tag from the fif file see Table 10 16 taginfo Contains the information about one tag see Table 10 17 directory Contains the tag directory as a tree structure see Table 10 18 id A fif ID see Table 10 19 named matrix Contains a matrix with names for rows and or columns see Table 10 20 A named matrix is used to store e g SSP vectors and forward solutions trans A 4 x 4 coordinate transformation matrix operating on augmented column vectors Indication of the coordinate frames to which this transformation relates is included see Table 10 21 dig A Polhemus digitizer data point see Table 10 22 coildef The coil definition structure useful for forward calculations and array visualization see Table 10 23 For more detailed information on coil definitions see Section 5 8 ch Channel information structure see Table 10 24 proj Signal space projection data see Table 10 25 comp Software gradiometer compensation data see Table 10 26 measurement info Translation of the FIFFB_MEAS_ INFO entity see Table 10 27 This data structure is returned by fiff_read_meas_info 261 10 The Matlab toolbox surf COV fwd inv Used to represent triangulated surfaces and cortical source spaces Table 10 28 Used for storing covariance matrices Table 10 29 Forward solution data returned
96. threshold Value histogram This part of the dialog shows the distribution of the currently shown estimate values over the surface The histogram is colored to reflect the current scale settings The fthresh fmid and fmax values are indicated with vertical bars The histogram is updated when the dia log 1s popped up and when the estimate type to show changes not at every new time point selection The Refresh button makes the histo gram current at any time Color scale These text fields control the color scale as described in Table 7 1 Options Various options controlling the estimates Parameter eng fthresh If the value is below this level it will not be shown fmid Positive values at this level will show as red Negative values will be dark blue fmax Positive values at and above this level will be bright yellow Negative values will be bright blue Table 7 1 The color scale parameters MSH MNE 177 Interactive analysis fmult Apply this multiplier to the above thresh olds Default is 1 for statistical maps and 17 for currents MNE The vertical bar locations in the histogram take this multi plier into account but the values indicated are the threshold parameters without the multiplier tcmult The upper limit of the timecourse vertical scale will be tC nut J mut max Table 7 1 The color scale parameters afato MNE preferences MIME preferences SNR estimate aa current std aase 10
97. tion files which can be used to ignore all magnetometer or all gradiometer channels in Vectorview measurements These files are called vv grad only bad and vv_mag_only bad respectively Both files are located in SMNE_ROOT share mne templates 3 14 Analyzing the data Once all the preprocessing steps described above have been completed the inverse operator computed can be applied to the MEG and EEG data and the results can be viewed and stored in several ways 1 The interactive analysis tool mne_analyze can be used to explore the data and to produce quantitative analysis results screen snapshots and MSH MNE The Cookbook al MSH MNE QuickTime movie files For comprehensive information on mne_analyze please consult Chapter 7 The command line tool mne_make_movie can be invoked to produce QuickTime movies and snapshots mne_make_movie can also output the data in the stc movies and w snapshots formats for subsequent processing Furthermore subject to subject morphing is included in mne_make_movie to facilitate cross subject averaging and comparison of data among subjects mne_make_movie is described in Section 6 5 The command line tool mne_make_movie can be employed to interro gate the source estimate waveforms from labels ROIs The mne_make_movie tool can be also used to create movies from stc files and to resample stc files in time The mne_compute_raw_inverse tool can be used to produce fif files
98. to the subject matter hereof and super cedes any prior or contemporaneous oral or written agreements with respect thereto Sections 2 4 6 8 9 11 shall survive any termination of this Agreement This Agreement may be modified or amended only in a writing signed by duly authorized representatives of both Parties hereto The invalidity or unenforceability of any provision of this Agreement shall not affect any other provision hereof This Agreement and the license granted hereunder may not be assigned 351 E Licence agreement 352 MSH MNE
99. triangles increases by a factor of four in each subdivision starting from 20 triangles in an icosahedron and 8 MSH MNE The forward solution al MSH MNE triangles in an octahedron Since the number of vertices on a closed surface iS N et Ng 4 2 the number of vertices in the kth subdivision of an icosahedron and an octahedron are 10 4 2 and fee 45D respectively The recommended values for lt number gt and the corresponding number of source space locations are listed in Table 3 1 all Include all nodes to the output The active dipole nodes are identi fied in the fif file by a separate tag If tri files were used as input the output file will also contain information about the surface triangula tion This option is always recommended to include complete infor mation Src lt name gt Output file name Use a name lt dir gt lt name gt src fif Note If both ico and spacing options are present the later one on the command line takes precedence Note Due to the differences between the FreeSurfer and MNE libraries the number of source space points generated with the spacing option may be different between the current version of MNE and versions 2 5 or earlier using Spacing option to mne_setup_source_space if the FreeSurfer surfaces employ the old quadrangle format or if there are topological defects on the surfaces All new FreeSurfer surfaces are speci fied as triangular tessellations and are e of defec
100. up the topographical display of epochs extracted from the raw data see Section 4 12 Show averages Brings up the topographical display showing averaged data These data may include data averaged in the current mne_browse_raw ses sion or those loaded from files see Section 4 4 2 Show event list Brings up a window containing a list of the currently defined events Clicking on an event in the list the event is selected a green cursor appears at the event and the event is brought to the middle of the raw data display The event list displayed can be also restricted to 67 4 Processing raw data user defined events annotations and user defined events can be deleted For further information see Section 4 10 Show annotator Brings up a window which allows adding new events to the data with annotations or comments For details see Section 4 10 Manage averages Brings up a dialog to control the averaged data sets see Section 4 15 Start mne_analyze Start interaction between mne_browse_raw and mne_analyze For details see Section 4 18 Quit mne_analyze Quits the mne_analyze program started with Start mne_analyze 4 8 The Help menu The contents of the Help menu is shown in Figure 4 13 Help On version On license About current data Why the beep Figure 4 13 The Help menu On version Displays the version and compilation date of the program On license Displays
101. visible on any of the surfaces displayed in the main surface display Time points can be picked in any of the surfaces As a result the corresponding timecourses will be shown in the MNE ampli tude window see Section 7 13 167 Ea Interactive analysis 7 10 The viewer 7 10 1 Overview k X Viewer Canvas EEG step 10u MEG step 50 0fT Adjust view Output a A 7 fpo Options Rescale Reload ma nov Figure 7 18 The viewer window with a visualization of MEG and EEG contour maps When Windows Show viewer is selected the following additional sur faces will be loaded The left and right hemisphere pial surfaces The surface representing the inner helmet shaped wall of the dewar on which the MEG sensors are located 3 The scalp surface and 4 The BEM surfaces NO The scalp surface is loaded from the file bem lt subject gt head fif under the subject s FreeSurfer directory This surface is automatically pre pared if you use the watershed algorithm as described in Section A 1 If you have another source for the head triangulation you can use the utility mne_surf2bem to create the fif format scalp surface file see Section 5 6 168 MSH MNE Interactive analysis 7 MSH MNE If a file called bem lt subject gt bem fif under the subject s FreeSurfer directory 1s present mne_analyze tries to load the BEM surface triangula tions from there This file can be a symbolic link to one
102. ways to create this file 1 Use the mne_make_fiducial_file m Matlab function not yet written to create this file 2 Copy a MRI description file with the MEG MRI coordinate transfor mation created with MRIlab typically SUBJECTS_DIR SUBJECT mri T1 neuromag sets COR lt date gt fif to SUBJECTS_DIR SUB JECT bem SUBJECT fiducials fif 3 For the average subject fsaverage copy the fsaverage fiducials fif file provided with mne_analyze in place see Section 7 19 7 17 Viewing continuous HPI data 660 A Show continuous HPI data _ Continuous HFI data 116 880 s GOF 99 91 1 Origin movement 12 2 mm z Angular velocity 1 2 deqg sec Coil movements 3 1 mm min 51 1 mm max 36 0 mm avwe 40 4 mm median Movement fron initial head head Transform now MIEG device gt head O 996466 0 015203 0 056570 45 mm DSSS066 B01bseY ObSsse6e 12mm 0 008745 0 917056 03995662 714mm 0 029721 0 955090 e 10 73 mm O 058214 0 5968468 0 915333 5766 mm 0 030735 0 354007 0 934736 5 76 mm O O00000 8 000000 O 000000 1 00 O O00000 O 000000 0 000000 1 00 Overview Hh NIMA Ape nil A Ud Ait i g Value 0 9 1 0 Angular velocity 0 20 0 deg sec W Y Average coil seai 50 0 mm a 7 118 _A_ Figure 7 29 Continuous HPI data overview The newest versions of Neuromag software allow continuous acquisition of signals from the HPI coils On the basis of these data the relative posi tion of the d
103. 102 check Check that the surfaces are complete and that they do not intersect This is a recommended option For more information see Section 5 6 4 checkmore In addition to the checks implied by the check option check Skull and skull thicknesses For more information see Section 5 6 4 fif lt name gt The output fif file containing the BEM These files normally reside in the bem subdirectory under the subject s mri data A name ending with bem fi f is recommended Surface options These options can be specified after each Surf or tri option to define details for the corresponding surface Swap Swap the ordering or the triangle vertices The standard convention in the MNE software is to have the vertices ordered so that the vec tor cross product of the vectors from vertex 1 to 2 and 1 to 3 gives the direction of the outward surface normal Text format triangle files produced by the some software packages have an opposite order For these files the swap option is required This option does not have any effect on the interpretation of the FreeSurfer sur face files specified with the surf option sigma lt value gt The conductivity of the compartment inside this surface in S m shift lt value mm gt Shift the vertices of this surface by this amount given in mm in the outward direction i e in the positive vertex normal direction meters The vertex coordinates of this surface are given in met
104. 12 A1 IRO1 NS44319 01 and 2RO1 NS37462 05 ell as by Department of Energy under Award Number DE FG02 99ER62764 to The MIND Insti tute a Introduction 10 MSH MNE CHAPTER2 Overview 2 1 List of components The principal components of the MNE Software and their functions are listed in Table 2 1 Documented software is listed in italics Table 2 2 lists various supplementary utilities mne_analyze An interactive analysis tool for computing source esti mates see Chapter 7 Average data across subjects see Section 8 6 2 mne_browse_raw Interactive raw data browser Includes filtering offline averaging and computation of covariance matrices see Chapter 4 mne_compute_mne Computes the minimum norm estimates see Section B 3 1 Most of the functionality of mne_compute_mne is included in mne_make_movie mne_compute_raw_inverse Compute the inverse solution from raw data see Section 6 6 mne_convert_mne_data Convert MNE data files to other file formats see Section 9 12 mne_do_forward_solution Convenience script to calculate the forward solution matrix see Section 3 11 mne_do_inverse_operator Convenience script to compute the inverse operator decomposition see Section 3 13 mne_forward_solution Calculate the forward solution matrix see Section 5 9 mne_inverse_operator Compute the inverse operator decomposition see Section 6 4 mne_make_movie Make movies in batch mode see Section 6 5 mne_make_source_space Create
105. 3 11 4 Importing Magnes compensation channel data 216 Creating software gradient compensation data 217 Importing KIT MEG system data anaana anana aana 218 Importing EEG data saved in the EDF EDF or BDF format 221 OvervieW a4 c c0ccau guste ee mned a 221 Using mne_edfafiff 0 0 eee 222 Post conversion taSkS 0 0 0 eee ees 223 Importing EEG data saved in the Tufts University format 224 Importing BrainVision EEG data 00005 225 Converting eXimia EEG data 0 cc eee ee 226 Converting digitization data 0 00000es 226 The hpts format 0 0 0 ee 227 Converting volumetric data into an MRI overlay 228 Listing source space data ccc eee eens 229 Listing BEM mesh data 0 00 cece eee eee 230 Converting surface data between different formats 231 command line options 2 0 00 eee eee 231 Converting MRI data into the fif format 234 Collecting coordinate transformations into one file 234 Converting an ncov covariance matrix file to fiff 235 Converting a lisp covariance matrix to fiff 236 The MNE data file conversion tool 0005 236 Command line options 0 00 ce ee 237 Guide to combining options 0 00 eee eee 239 Matlab data structures 0 0 0 ccc ee 240 Converting raw data to Matlab format 243 C
106. Apts file will be ignored hpts lt filename gt Specifies the name of an electrode position file in the Apts format discussed in Section 9 3 1 The mandatory entries are the fiducial marker locations and the EEG electrode locations It is recom mended that electrode channel names instead of numbers are used to label the EEG electrode locations When this option is encoun tered on the command line any previously specified elp file will be ignored meters Assumes that the digitization data in an Apts file is given in meters instead of millimeters fif lt filename gt Specifies the name of the fif file to be output 9 2 8 3 Post conversion tasks This section outlines additional steps to be taken to use the EDF EDF BDF file is converted to the fif format in MNE 1 Some of the channels may not have a digitized electrode location asso ciated with them If these channels are used for EOG or EMG measure ments their channel types should be changed to the correct ones using the mne_rename_channels utility see Section 11 4 5 EEG channels which do not have a location associated with them should be assigned to be MISC channels 2 After the channel types are correctly defined a topographical layout file can be created for mne_browse_raw and mne_analyze using the mne_make_eeg_layout utility see Section 11 6 3 The trigger channel name in BDF files is Status This must be speci fied with the digtrig option or with he
107. EG fT cm Sets the scale for MEG planar gradiometer channels in fT cm All scale values are defined from zero to maximum i e the viewport where signals are plotted in have the limits lt scale value gt MEG axmult cm The scale for MEG magnetometers and axial gradiometers is defined by multiplying the gradiometer scale by this number yield ing units of fT EEG uV The scale for EEG channels in uV EOG uV The scale for EOG channels in uV ECG mV The scale for ECG channels in mV EMG mV The scale for EMG channels in mV MISC V The scale for MISC channels in V Time span s The length of raw data displayed in the main window at a time Show stimulus markers Draw vertical lines at time points where the digital trigger channel has a transition from zero to a nonzero value Segment min time s It is possible to show data segments in the topographical full view layout see below This parameter sets the starting time point rela tive to the selected time to be displayed Segment max time s This parameter sets the ending time point relative to the current time to be displayed in the topographical layout Show segments in full view Switches on the display of data segments in the topographical lay out Show segments in sample view Switches on the display of data segments in a sidebar to the right of the main display MSH MNE Processing raw data 4 4 5 3 MSH MNE Show channel n
108. HE GENERAL HOSPITAL CORPORATION ACADEMIC RESEARCH USE SOFTWARE LICENSE AGREEMENT FOR BINARY CODE By downloading and or using the MNE software which is the subject of this Agreement the Software you hereby accept and agree to all of the terms and conditions of this Agreement As used in this Agreement you means the individual who clicks the I accept button required as a condition of downloading the Software and the not for profit or govern mental institution or entity which employs or is otherwise affiliated with such individual at the time of such download the Institution 1 License Grant Subject to all of the terms and conditions of this Agree ment The General Hospital Corporation d b a Massachusetts General Hospital The Brigham and Women s Hospital Inc Licensor hereby grants you a non exclusive non transferable non sublicensable license under Licensor s rights in the Software to copy and use the binary code of the Software solely for research and educational pur poses under your direction at the Institution Research and Educa tional Purposes which term shall include company sponsored research conducted by you in accordance with Institution s policies 2 No Transfer You may not sell license distribute rent lease offer on an ASP or service bureau basis grant a security interest in or otherwise transfer the Software to any third party or use the Software for any commercial
109. Help n a Figure 4 8 Dialog to create a new channel selection The components of the selection creation dialog shown in Figure 4 8 have the following functions List of channel names The channels selected from this list will be included in the new channel selection A selection can be extended with the control key A range of channels can be selected with the shift key The list con tains both the original channels actually present in the file and the names of the channels in currently loaded derivation data see Section 4 4 12 MSH MNE Processing raw data 4 Regexp This provides another way to select channels By entering here a regular expression as defined in IEEE Standard 1003 2 POSIX 2 all channels matching it will be selected and added to the present selection An empty expression deselects all items in the channel list Some useful regular expressions are listed in Table 4 1 In the present version regular matching does not look at the derived chan nels Name This text field specifies the name of the new selection Select Select the channels specified by the regular expression The same effect can be achieved by entering return in the Regexp Add Add a new channel selection which contains the channels selected from the channel name list The name of the selection is specified with the Name text field Selects all MEG channels Selects all EEG channels Selects all MEG channels whose names end with th
110. I volume volume file in mgh or mgz format This file pro vides T The transformation T will be read from the talair ach xfm file referred to in the MRI volume The fixed transforms T_ and T will be also created out lt name gt Specifies the output file If this option is not present the collected transformations will be output on screen but not saved 9 10 Converting an ncov covariance matrix file to fiff The ncov file format was used to store the noise covariance matrix file The MNE software requires that the covariance matrix files are in fif for mat The utility mne_convert_ncov converts ncov files to fif format The command line options are version Show the program version and compilation date help List the command line options ncov lt name gt The ncov file to be converted meas lt name gt A fif format measurement file used to assign channel names to the noise covariance matrix elements This file should have precisely the same channel order within MEG and EEG as the ncov file Typ ically both the ncov file and the measurement file are created by the now mature off line averager meg_average 235 9 Data conversion 236 9 11 Converting a lisp covariance matrix to fiff The utility mne_convert_Ispcov converts a LISP format noise covariance file produced by the Neuromag signal processor graph into fif format The command line options are version Show the program version and compilat
111. If the name contains multiple words enclose it in quotation marks like this The name will appear in the average manager window listing in the interactive ver sion of the program and as a comment averaging category section in the output file abs Calculate the absolute values of the data in the epoch before adding it to the average stderr The standard error of mean will be computed for this category and included in the output fif file Note Specification of the baseline limits does not any more imply the estimation of the standard error of mean Instead the stderr parameter is required to invoke this option 4 14 Description files for covariance matrix estimation Covariance matrix estimation is controlled by a another description file very similar to the average definition A example of a covariance descrip tion file can be found in the directory MNE ROOT share mne mne browse raw templates MSH MNE Processing raw data 4 MSH MNE 4 14 1 4 14 2 Overall format Any line beginning with the pound sign in this description file is a comment Each parameter in the description file is defined by a keyword usually followed by a value Text values consisting of multiple words separated by spaces must be included in quotation marks The case of the keywords in the file does not matter The ending cov is suggested for the covariance matrix description files The general format of the description file is cov
112. MEG measurement surface i e inner surface of the dewar EEG electrodes The EEG electrode locations These will be only available 1f your data set contains EEG channels MEG sensors Outlines of MEG sensors MEG field map Estimated contour map of the magnetic field component normal to the helmet surface or normal to the scalp see Section 7 11 EEG potential map Interpolated EEG potential map on the scalp surface see Section 7 11 MSH MNE Interactive analysis ZA MSH MNE 7 11 7 11 1 Activity estimates Current estimates on the pial surface Magnetic field and electric potential maps Overview In mne_analyze the magnetic field and potential maps displayed in the viewer window are computed using an MNE based interpolation tech nique This approach involves the following steps 1 Establish an inverse operator to compute a minimum norm solution on a spherical surface using a spherically symmetric forward model Instead of assuming a discrete grid of sources a continuous distribu tion of tangential currents is employed In this case the lead field dot products can be computed in closed form Separate solutions are com puted for MEG and EEG 2 The normal component of the magnetic field or the electric potential on the helmet or head surface is computed from the MEG based and EEG based MNE Since the MNE predicts the original measurements accu rately it can also interpolate and extrapolate the data reliably T
113. MNE software User s Guide Version 2 7 December 2009 Matti Hamaldinen MGH HMS MIT Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown Massachusetts USA This document contains copyrighted information The author reserves the right to make changes in the specifications or data shown herein at any time without notice or obligation The author makes no warranty of any kind with regard to this document The author shall not be liable for errors contained herein or direct indirect incidental or consequen tial damages in connection with the furnishing performance or use of this document Identifier Version Date Printing History Ist edition 2nd edition 3rd edition Ath edition Sth edition 6th edition 7th edition 8th edition 9th edition 10th edition 11th edition 12th edition 12th edition MSH MNE MSH MNE MSH MNE MSH MNE MSH MNE MSH MNE MSH MNE MSH MNE MSH MNE MSH MNE MSH MNE MSH MNE MSH MNE 14 1 2 1 3 1 4 1 5 1 6 E7 2d 2 2 24 2D 2 6 2l August 2001 April 2002 July 2002 October 2002 November 2002 December 2002 March 2003 April 2005 August 2005 December 2005 December 2006 March 2009 December 2009 MSH MNE Contents Chapter 1 Introduction Chapter 2 Overview 2 1 List of components 2 2 File formats 2 3 Conventions 2 4 User environment Chapter 3 The Cookbook 3 1 Overview 3 2 Selecting the subject
114. MSH MNE The purpose of the utility mne_compute_raw_inverse is to compute inverse solutions from either evoked response or raw data at specified ROIs labels and to save the results in a fif file which can be viewed with mne_browse_raw read to Matlab directly using the MNE Matlab Tool box see Chapter 10 or converted to Matlab format using either mne_convert_mne_data mne_raw2mat or mne_epochs2mat see Chapter 9 Command line options version Show the program version and compilation date help List the command line options in lt filename gt Specifies the input data file This can be either an evoked data file or a raw data file bmin lt time ms gt Specifies the starting time of the baseline In order to activate base line correction both bmin and bmax options must be present This option applies to evoked data only bmax lt time ms gt Specifies the finishing time of the baseline This option applies to evoked data only set lt number gt The data set condition number to load This is the sequential num ber of the condition You can easily see the association by looking at the condition list in mne_analyze when you load the file Inv lt name gt Load the inverse operator decomposition from here nave lt value gt Specifies the effective number of averaged epochs in the input data Le as discussed in Section 6 3 If the input data file is one pro 141 6 The current estimates d
115. Number of rows is either nsource fixed source orientations or 3 nsource all source orientations sing double nchan The singular values i e the diagonal values of A see Section 6 2 5 eigen_leads double nchan The matrix V see Section 6 2 5 T eigen_fields double nchan nchan The matrix U see Section 6 2 5 noise_Cov The noise covariance matrix C source_COV The source covariance matrix R src The description of the source spaces mri_head_t trans Transformation from the MRI coordinate frame to the Neuromag head coordinate frame projs proj The SSP vectors which were active when the decomposition was computed double nchan The projection operator computed using projs whitener A sparse matrix containing the noise normalization factors Dimension is either nsource fixed source orientations or 3 nsource all source orientations double nchan The diagonal matrix T see Section 6 2 5 noisenorm double A sparse matrix containing the noise normalization factors Dimension is either nsource fixed source orientations or 3 nsource all source orientations Table 10 31 The inv structure Note The fields proj whitener reginv and noisenorm are filled in by the routine mne_prepare_inverse_operator MSH MNE 273 10 The Matlab toolbox 10 3 On line documentation for individual routines Each of the routines listed in Tables 10 1 10 14 has on line documenta tion accessible by
116. PRIOR COV 3 Indicates a covariance matrix associ ated with MRI priors FIFFV_MNE_ SIGNAL COV 4 Indicates the data signal noise cova riance matrix FIFFV_MNE_DEPTH_PRIOR_COV 5 Indicates the depth prior depth weight ing covariance matrix FIFFV_MNE_ORIENT_PRIOR_COV Indicates the orientation loose orienta tion constrain prior covariance matrix FIFFV_PROJ_ITEM_NONE The nature of this projection item is unknown FIFFV_PROJ_ITEM_FIELD 1 This is projection item is a generic field pattern or field patters Table 10 15 FIFF constants 264 MSH MNE The Matlab toolbox wane ve eeton FIFFV_PROJ_ITEM_DIP_FIX ENTE P ame This projection item is the field of one dipole FIFFV_PROJ_ITEM_DIP_ROT This projection item corresponds to the fields of three or two orthogonal dipoles at some location FIFFV_PROJ_ITEM_HOMOG_GRAD This projection item contains the homogeneous gradient fields as seen by the sensor array FIFFV_PROJ_ITEM_HOMOG_FIELD This projection item contains the three homogeneous field components as seen by the sensor array FIFFV_MNE_PROJ_ITEM_EEG_AVREF 10 This projection item corresponds to the average EEG reference Table 10 15 FIFF constants Feia oattype Desorption The kind of the data item The data type used to represent the data Size of the data in bytes Byte offset of the next tag in the file Table 10 16 The tag structure roa omame beeen Table 10 17 The taginfo structure
117. Proceed to mne_setup_forward_model Use the surf and noswap options Note If left and right are flipped in BrainSuite use the flip option in mne_convert_surface to set the coordinate transformation correctly Tip The BrainSuite scalp surface can be also used for visualization in mne_analyze see Section 7 16 1 MSH MNE APPENDIX B B 1 Setup at the Martinos Center This Appendix contains information specific to the Martinos Center setup User environment In the Martinos Center computer network the 2 7 version of MNE is located at usr pubsw packages mne stable To use this version follow Section 2 4 substituting usr pubsw packages mne stable for lt MNE gt and usr pubsw packages matlab current for lt Matlab gt For most users the default shell is tesh Tip A new version of MNE is build every night from the latest sources This version is located at usr pubsw packages mne nightly B 2 Using Neuromag software B 2 1 Software overview MSH MNE The complete set of Neuromag software is available on the LINUX work stations The programs can be accessed from the command line see Table B 1 The corresponding manuals located at SNEUROMAG ROOT manuals are listed in Table B 2 moue eseriton Source modelling Table B 1 Principal Neuromag software modules 325 B Setup at the Martinos Center 326 B 2 2 Xplotter pdf GraphReference pdf Table B 2 List of Neuromag software manuals
118. SH MNE 93 a The forward solution 94 The coordinate systems related to MEG EEG data are Head coordinates This is a coordinate system defined with help of the fiducial land marks nasion and the two auricular points In fif files EEG elec trode locations are given in this coordinate system In addition the head digitization data acquired in the beginning of an MEG MEG EEG or EEG acquisition are expressed in head coordinates For details see Section 5 2 Device coordinates This is a coordinate system tied to the MEG device The relation ship of the Device and Head coordinates is determined during an MEG measurement by feeding current to 3 5 head position indi cator HPI coils and by determining their locations with respect to the MEG sensor array from the magnetic fields they generate Sensor coordinates Each MEG sensor has a local coordinate system defining the orien tation and location of the sensor With help of this coordinate sys tem the numerical integration data needed for the computation of the magnetic field can be expressed conveniently as discussed in Section 5 8 The channel information data in the fif files contain the information to specify the coordinate transformation between the coordinates of each sensor and the MEG device coordinates The coordinate systems related to MRI data are Surface RAS coordinates The FreeSurfer surface data are expressed in this coordinate system The origin of th
119. Scroll backward or forward in the data by one screen With Alt key Command or Apple key in the Mac keyboard the amount of scroll ing will be 1s instead of the length of one screen If shift key is held down with the trackball both left right and up down movements scroll the data in time Note The trackball and mouse wheel functionality is dependent on your X server settings On Mac OSX these settings are normally correct by default but on a LINUX system some adjustments to the X server settings maybe necessary Consult your system administrator or Google for details MSH MNE Processing raw data 4 MSH MNE 4 10 4 10 1 4 10 2 Events and annotations Overview In mne_browse_raw and mne_process_raw events mark interesting time points in the data When a raw data file is opened a standard event file is consulted for the list of events If this file is not present the digital trigger channel defined by the digtrig option or the MNE_TRIGGER CH NAME environment variable is scanned for events For more information see Sections 4 2 1 and 4 4 1 In addition to the events detected on the trigger channel it is possible to associate user defined events to the data either by marking data points interactively as described in Section 4 10 4 or by loading event data from files see Section 4 10 3 Especially if there is a comment associated with a user defined event we will sometimes call it an annotation If a data files has ann
120. Simple Model Format output file For details of this format see http people scs fsu edu burkardt data smf txt Note Multiple output options can be specified to produce outputs in sev eral different formats with a single invocation of mne_convert_surface The coordinate transformation file specified with the trans should contain a 4 x 4 coordinate transformation matrix Ki Riz 13 Xo r Ei 13 413 Yo Riz A13 R13 Zo 0 0 0 1 defined so that if the augmented location vectors in the dfs file and MRI coordinate systems are denoted by rg and ap Yafs Zafs respectively r MRI XMRI Yuri ZMRI rMRI Tags MSH MNE 233 9 Data conversion 234 9 8 Converting MRI data into the fif format The utility mne_make_cor_set creates a fif format MRI description file optionally including the MRI data using FreeSurfer MRI volume data as input The command line options are version Show the program version and compilation date help List the command line options dir lt directory gt Specifies a directory containing the MRI volume in COR format Any previous mgh options are cancelled when this option is encountered withdata Include the pixel data to the output file This option is implied with the mgh option mgh lt name gt An MRI volume volume file in mgh or mgz format The with data option is implied with this type of input Furthermore the T transformation the Talairach transformation
121. Since the surface relations are transitive it is enough to check that the outer skull surface is inside the skin surface and that the inner skull surface is inside the outer skull one 3 The extent of each of the triangulated volumes is checked If the extent is smaller than 50 mm an error is reported This may indicate that the vertex coordinates have been specified in meters instead of millimeters 5 7 Computing the BEM geometry data The utility mne_prepare_bem_model computes the geometry information for BEM This utility is usually invoked by the convenience script mne_setup_forward_model see Section 3 7 The command line options are bem lt name gt Specify the name of the file containing the triangulations of the BEM surfaces and the conductivities of the compartments The stan dard ending for this file is bem fi f and it is produced either with the utility mne_surf2bem Section 5 6 or the convenience script mne_setup_forward_model see Section 3 7 Sol lt name gt Specify the name of the file containing the triangulation and con ductivity information together with the BEM geometry matrix com puted by mne_prepare_bem_model The standard ending for this file is bem sol fif method lt approximation method gt Select the BEM approach If lt approximation method gt is con stant the BEM basis functions are constant functions on each tri angle and the collocation points are the midpoints of the triangles With linea
122. TF Polhemus data The CTF MEG systems store the Polhemus digitization data in text files The utility mne_ctf_dig2fiff was created to convert these data files into the fif and hpts formats The input data to mne_ctf_dig2fiff is a text file which contains the coordi nates of the digitization points in centimeters The first line should contain a single number which is the number of points listed in the file Each of the following lines contains a sequential number of the point followed by the three coordinates mne_ctf_dig2fiff ignores any text following the z coordinate on each line If the numfids option is specified the first three points indicate the three fiducial locations 1 nasion 2 left auric ular point 3 right auricular point Otherwise the input file must end with three lines beginning with left right or nasion to indicate the locations of the fiducial landmarks respectively Note The sequential numbers should be unique within a file I particular the numbers 2 and 3 must not be appear more than once if the num fids options is used The command line options for mne_ctf_dig2 fiff are version Show the program version and compilation date help List the command line options dig lt name gt Specifies the input data file in CTF output format numfids Fiducial locations are numbered instead of labeled see above hpts lt name gt Specifies the output hpts file The format of this text f
123. The Cookbook 38 fmrithresh lt value gt This option is mandatory and has an effect only if a weighting func tion has been specified with the fmri option If the value is in the a priori files falls below this value at a particular source space point the source covariance matrix values are multiplied by the value specified with the fmrioff option default 0 1 Other wise it is left unchanged fmrioff lt value gt The value by which the source covariance elements are multiplied if the a priori weight falls below the threshold set with fmrithresh see above Srccov lt name gt Use this diagonal source covariance matrix By default the source covariance matrix is a multiple of the identity matrix This option 1s irrelevant to most users proj lt name gt Include signal space projection information from this file Inv lt name gt Save the inverse operator decomposition here By default the script looks for a file whose name is derived from the forward solution file by replacing its ending fwd fif by lt options gt inv f1f where lt options gt includes options meg eeg and fixed with the double dashes replaced by single ones Important If bad channels are included in the calculation strange results may ensue Therefore it is recommended that the data to be analyzed is carefully inspected with to assign the bad channels correctly Tip For convenience the MNE software includes bad channel designa
124. The number can be given in decimal or hexadecimal format beginning with Ox or OX For example the value 255 OxFEF means that only the lowest order byte usually trigger lines 1 8 or bits O 7 will be considered includetrig Add the digital trigger channel to the list of channels to output This option should not be used if the trigger channel is already included in the selection specified with the sel option filtersize lt size gt Adjust the length of the FFT to be applied in filtering The number will be rounded up to the next power of two If the size is N the corresponding length of time is N f where f is the sampling frequency of your data The filtering procedure includes overlapping tapers of length N 2 so that the total FFT length will actually be 2N The default value is 4096 highpass lt value Hz gt Highpass filter frequency limit If this is too low with respect to the selected FFT length and data file sampling frequency the data will not be highpass filtered You can experiment with the interactive version to find the lowest applicable filter for your data This value can be adjusted in the interactive version of the program The default is 0 1 e no highpass filter in effect highpassw lt value Hz The width of the transition band of the highpass filter The default is 6 frequency bins where one bin is f 2N lowpass lt value Hz gt Lowpass filter frequency limit This value can be adjuste
125. To access the Neuromag software on the LINUX workstations in the Mar tinos Center say in tcsh or csh source space orsay 8 megdev Neuromag LINUX neuromag setup csh or in POSIX shell space orsay 8 megdev Neuromag LINUX neuromag setup sh Using MRilab for coordinate system alignment The MEG MRI coordinate system alignment can be also accomplished with the Neuromag tool MRIlab part of the standard software on Neuro mag MEG systems In MRIlab the following steps are necessary for the coordinate system alignment 1 Load the MRI description file COR fif from subjects sample mri Tl neuromag sets through File Open 2 Open the landmark setting dialog from Windows Landmarks 3 Click on one of the coordinate setting fields on the Nasion line Click Goto Select the crosshair tool and move the crosshair to the nasion Click Get 4 Proceed similarly for the left and right auricular points Your instructor will help you with the selection of the correct points 5 Click OK to set the alignment 6 Load the digitization data from the file sample audvis raw fif or sample audvis ave fif the on line evoked response average file in MEG sample through File Import Isotrak data Click Make points to show all the digitization data on the MRI slices MSH MNE Setup at the Martinos Center B MSH MNE 7 Check that the alignment is correct by looking at the locations of the digitized points are reasonable Adjust the landma
126. _volume_source_space to an MRI overlay see Section 9 4 D 3 4 8 mne_volume_source_space Create a a grid of source points within a volume see Section 5 5 mne_volume_source_space also optionally creates a trilinear interpolator matrix to facilitate converting values a distribution in the volume grid into an MRI overlay using mne_volume_data2mri see Section 9 4 D 3 4 9 mne_copy_processing_history This new utility copies the processing history block from one data file to another see Section 11 4 8 MSH MNE Release notes D MSH MNE D 4 Release notes for MNE software 2 7 D 4 1 Software engineering There have been two significant changes in the software engineering since MNE Version 2 6 e CMake is now used in building the software package and e Subversion SVN is now used for revision control instead of Concur rent Versions System CVS These changes have the effects on the distribution of the MNE software and setup for individual users e There is now a separate software package for each of the platforms supported e The software is now organized completely under standard directories bin lib and share In particular the directory setup mne has been moved to share mne and the directories app defaults and doc are now under share All files under share are platform independent e The use of shared libraries has been minimized This alleviates com patibility problems across operating system versions e The setup s
127. a fif source space description file see Section 5 4 Table 2 1 The software components MSH MNE 11 A Overview mne_process_raw A batch mode version of mne_browse_raw see Chapter 4 mne_redo_file Many intermediate result files contain a description of their production environment Such files can be recre ated easily with this utility This is convenient if for example the selection of bad channels is changed and the inverse operator decomposition has to be recalcu lated mne_redo_file_nocwd Works like mne_redo_file but does not try to change in to the working directory specified in the production environment mne_setup_forward_model Set up the BEM related fif files see Section 3 7 mne_setup_mri A convenience script to create the fif files describing the anatomical MRI data see Section 3 4 mne_setup_source_space A convenience script to create a source space description file see Section 3 5 Show information about the production environment of a file Table 2 1 The software components me ese Add patch information to a source space file see Section 11 7 mne_add_to_meas_ info Utility to add new information to the measurement info block of a fif file The source of information is another fif file mne_add_triggers Modify the trigger channel STI 014 in a raw data file see Section 11 4 6 The same effect can be reached by using an event file for averaging in mne_process_raw and mne_browse_raw m
128. actise unknown We can express this by writing R R A which yields the inverse operator f M RG GRG C where the unknown current amplitude is now interpreted in terms of the regularization parameter Small K corresponds to large current amplitudes and complex estimate current patterns while a large 1 means the amplitude of the current is limited and a simpler smooth current esti mate is obtained We can arrive in the regularized linear inverse operator also by minimiz ing the cost function ape _ S e e A j R i where the first term consists of the difference between the whitened mea sured data see Section 6 2 3 and those predicted by the model while the second term is a weighted norm of the current estimate It is seen that with increasing the source term receive more weight and larger dis crepancy between the measured and predicted data is tolerable 6 2 3 Whitening and scaling The MNE software employs data whitening so that a whitened inverse operator assumes the form m T M RG GRG 1 where G GG is the spatially whitened gain matrix The expected current values are j t Mx t where x t C x t is athe whit ened measurement vector at t The spatial whitening operator is obtained MSH MNE The current estimates Lo MSH MNE 6 2 4 with the help of the eigenvalue decomposition C UAU as C Ac UG In the MNE software the noise covariance matrix is store
129. after options unique to the interactive mne_browse_raw and batch mne_process_raw modes are listed Common options version Show the program version and compilation date help List the command line options cd lt dir gt Change to this directory before starting 41 4 Processing raw data raw lt name gt Specifies the raw data file to be opened This option is required for batch version mne_process_raw If a raw data file is not specified for the interactive version mne_browse_raw and empty interactive browser will open grad lt number gt Apply software gradient compensation of the given order to the data loaded with the raw option This option is effective only for data acquired with the CTF and 4D Magnes MEG systems If orders dif ferent from zero are requested for Neuromag data an error message appears and data are not loaded Any compensation already existing in the file can be undone or changed to another order by using an appropriate grad options Possible orders are 0 No compensa tion 1 3 CTF data and 101 Magnes data The same compen sation will be applied to all data files loaded by mne_process_raw For mne_browse_raw this applies only to the data file loaded by specifying the raw option For interactive data loading the soft ware gradient compensation is specified in the corresponding file selection dialog see Section 4 4 1 filtersize lt size gt Adjust the length of
130. ag software coil type 3024 is fully supported Therefore it is now safe to upgrade the data files to use the true coil type If the magnes option is specified the 4D Magnes magnetometer coil type 4001 is changed to 4D Magnes gradiometer coil type 4002 Use this option always and only if your Magnes data comes from a system with axial gradiometers instead of magnetometers The fif converter included with the Magnes system does not assign the gradiometer coil type correctly Note The effect of the difference between the coil sizes of magnetometer types 3022 and 3024 on the current estimates computed by the MNE soft ware is very small Therefore the use of mne_fix_mag_coil_types is not mandatory Modifying channel names and types mne_rename_channels Sometimes it is necessary to change the names types of channels in MEG EEG data files Such situations include e Designating an EEG as an EOG channel For example the EOG chan nels are not recognized as such in the fif files converted from CTF data files e Changing the name of the digital trigger channel of interest to STI 014 so that mne_browse_raw and mne_process_raw will recognize the cor rect channel without the need to specify the digtrig option or the MNE_TRIGGER_CH_NAME environment variable every time a data file is loaded The utility mne_rename_channels was designed to meet the above needs It recognizes the following command line options MSH MNE Miscellaneous ut
131. allows to change this prefix to lt name gt _ meg eeg Include MEG channels from the forward solution and noise covari ance matrix Include EEG channels from the forward solution and noise covari ance matrix Inv lt name gt Output the inverse operator data from the specified file into a mat file The source and noise covariance matrices as well as active channels have been previously selected when the inverse operator was created with mne_inverse_operator Thus the options meg eeg Ssenscov srccov noiseonly and bad do not affect the output of the inverse operator meas lt name gt Specifies the file containing measurement data to be output together with the inverse operator The channels corresponding to the inverse operator are automatically selected from the file if inv option is present Otherwise the channel selection given with sel option will be taken into account set lt number gt Select the data set to be output from the measurement file MSH MNE Data conversion 9 9 12 2 Desired output Required options bmin lt value ms gt Specifies the baseline minimum value setting for the measurement signal output bmax lt value ms gt Specifies the baseline maximum value setting for the measurement signal output Note The tmin and tmax options which existed in previous ver sions of mne_converted_mne_data have been removed If output of mea surement data is requ
132. ames Show the names of the channels in the topographical displays Text size Size of the channel number text as a fraction of the height of each viewport Show viewport frames Show the boundaries of the viewports in the topographical displays Show zeroline and zerolevel Show the zero level i e the baseline level in the topographical dis plays In addition the zero time point is indicated in the average views if it falls to the time range i e if the minimum of the time scale is negative and the maximum is positive Scale magnification for averages For average displays the scales are made more sensitive by this fac tor Average display baseline min ms Sets the lower time limit for the average display baseline This set ting does not affect the averages stored Average display baseline max ms Sets the upper time limit for the average display baseline This set ting does not affect the averages stored Use average display baseline Switches the application of a baseline to the displayed averages on and off Average time range min ms Sets the minimum time for the average display This setting is inac tive if Autoscale time range is on Average time range max ms Sets the maximum time for the average data display This setting is inactive if Autoscale time range is on Autoscale time range Set the average display time range automatically to be long enough to accommodate all data Colors Shows a dialog whic
133. ample data set e Chapter 13 contains a list of useful references for understanding the methods implemented in the MNE software 334 MSH MNE APPENDIx D Release notes MSH MNE D 1 D 1 1 D 1 2 D 1 3 This appendix contains a brief description of the changes in MNE soft ware in each major release Release notes for MNE software 2 4 Manual The manual has been significantly expanded and reorganized Chapter 7 describing mne_analyze has been added Chapter 12 contains instructions for analyzing the sample data set provided with the software Useful back ground material is listed in Chapter 13 Almost all utility programs are now covered in the manual General software changes The following overall changes have been made 1 A forward solution library independent of Neuromag software was written 2 The MEG sensor information is now imported from the coil definition file instead of being hardcoded in the software For details see Section 5 8 4 CTF and 4D Neuroimaging sensors are now supported The number of Neuromag based utilities was minimized 5 The LINUX port of Neuromag software modules was completely sepa rated from the MNE software and now resides under a separate direc tory tree 6 Support for topologically connected source spaces was added see Section 3 5 7 A lot of bugs were fixed e U File conversion utilities The following import utilities were added 335 D Release notes D 1
134. an 20 mm to the center of mass of the grid volume will be excluded as well as those closer than 10 mm to the surface Note that this guess grid is only used for establishing the initial guess the actual dipole fitting procedure does not constrain the solution to this grid When the Fit ECD button in the tool bar is clicked with a time point selected from the the response the optimal Equivalent Current Dipole parameters location orientation and amplitude are determined using the following algorithm l An initial guess for the location of the dipole is determined using the grid of locations determined in step 4 above At each guess dipole location the least squares error between the measured data and a dipole at that location is evaluated and the location corresponding to the smallest error is used as the initial guess location In this process the dipole amplitude parameters do not need to be explicitly calculated Using the Nelder Mead simplex optimization algorithm an optimal dipole location is determined with the sphere model used as the for ward model Again the dipole amplitude parameters are not explicitly present in the fitting procedure A second optimization interation using the boundary element model if available or the sphere model as the forward model is conducted The reason for repeating the optimization even with the sphere model is to reduce the likelihood of having been stuck in a local minimum of the l
135. analysis software installed mne_browse_raw is compatible with cliplab versions 1 2 13 and later Note The graphics output files will contain a text line stating of the time and vertical scales if the zero level time and or viewport frames have been switched on in the scales dialog see Section 4 5 2 4 13 Description files for off line averaging For averaging tasks more complex than those involving only one trigger the averaging parameters are specified with help of a text file This section describes the format of this file A sample averaging file can be found in SMNE ROOT share mne mne browse raw templates MSH MNE Processing raw data 4 MSH MNE 4 13 1 Overall format Any line beginning with the pound sign in this description file is a comment Each parameter in the description file is defined by a keyword usually followed by a value Text values consisting of multiple words separated by spaces must be included in quotation marks The case of the keywords in the file does not matter The ending ave is suggested for the average description files The general format of the description file is average lt common parameters gt category lt category definition parameters gt The file may contain arbitrarily many categories The word category interchangeable with condition Warning Due to a bug that existed in some versions of the Neuromag acquisition software the trigger line 8 is incorrectly decoded
136. ance file to fif see Section 9 10 Convert FreeSurfer and text format surface files into Matlab mat files see Section 9 7 mne_convert_surface Pick eigenvectors from a covariance matrix and create a signal space projection SSP file out of them see Section 11 9 mne_cov2pro Create a fif file containing software gradient compensation information from a text file see Section 9 2 6 mne_create_comp_data mne_ctf2fiff Convert a CTF ds folder into a fif file see Section 9 2 2 mne_ctf_dig2fiff Convert text format digitization data to fif format see Section 9 2 3 mne_dicom_essentials List essential information from a DICOM file This utility is used by the script mne_organize_dicom see Section A 2 1 mne_edf2fiff Convert EEG data from the EDF EDF BDF formats to the fif format see Section 9 2 8 mne_epochs2mat Apply bandpass filter to raw data and extract epochs for subsequent processing in Matlab see Section 9 14 Table 2 2 Utility programs MSH MNE 13 Overview mne_insert_4D_comp a cvorvicw mne_evoked_data_summary List summary of averaged data from a fif file to the standard output mne_eximia2fiff Convert EEG data from the Nexstim eXimia system to fif format see Section 9 2 11 mne_fit_sphere_to_surf Fit a sphere to a surface given in either fif or FreeSurfer for mat see Section 11 9 mne_fix_mag_coil_types Update the coil types for magnetometers in a fif file see Section 11 4 4 mn
137. and integ options tif lt name gt Produce tif snapshots This is the stem of the ouput file name The actual name is derived by stripping anything upto and including the last period from the end of lt name gt According to the hemisphere lh or rh is then appended The name of the view is indicated with lt viename gt Finally tif is added to indicate an rgb output file Files are produced for all picked times as dictated by the pick and integ options The tif output files are not com pressed Pass the files through an image processing program to com press them jpg lt name gt Produce jpg snapshots This is the stem of the ouput file name The actual name is derived by stripping anything upto and including the last period from the end of lt name gt According to the hemisphere lh or rh is then appended The name of the view is indicated with lt viename gt Finally jpg is added to indicate an rgb output file Files are produced for all picked times as dictated by the pick and integ options MSH MNE The current estimates a MSH MNE png lt name gt Produce png snapshots This is the stem of the ouput file name The actual name is derived by stripping anything upto and including the last period from the end of lt name gt According to the hemi sphere 1h or rh is then appended The name of the view is indi cated with lt viename gt Finally png is added to indic
138. annel list projs proj SSP operator data comps comp Software gradient compensation data p p p Table 10 27 The meas info structure sigma double The electrical conductivity of the compartment bounded by this surface This field is present in BEM surfaces only Number of vertices on the surface Number of triangles on the surface coord_frame int32 Coordinate frame in which the locations and orientations are expressed double np 3 The vertex locations nn double np 3 The vertex normals If derived surface data was not requested this is empty tris int32 ntri 3 Vertex numbers of the triangles in counterclockwise order as seen from the outside Table 10 28 The surf structure 270 MSH MNE The Matlab toolbox Field Data type Description nuse int32 Number of active vertices i e vertices included in a decimated source space int32 np Which vertices are in use int32 nuse Indices of the vertices in use curv double np Curvature values at the vertices If curvature information was not requested this field is empty or absent tri_area double ntr1 The triangle areas in m7 If derived surface data was not requested this field will be missing tri_cent double ntri 3 The triangle centroids If derived surface data was not requested this field will be missing tri_nn double ntri 3 The triangle normals If derived surface data was not requested this field will be missing nuse_tri int32 Number
139. are version Show the program version and compilation date help List the command line options file lt name gt Specify the measurement data file to be checked or modified dig lt name gt Name of the file containing the Polhemus digitizer information Default is the data file name fix By default mne_check_eeg_locations only checks for missing EEG locations locations close to the origin With fix mne_check_eeg_locations reads the Polhemus data from the speci fied file and copies the EEG electrode location information to the channel information records in the measurement file There is no 21 1 1 Miscellaneous utilities 2 8 harm running mne_check_eeg_locations on a data file even if the EEG channel locations were correct in the first place 11 4 4 Updating magnetometer coil types mne_fix_mag_coil_types 11 4 5 The purpose of mne_fix_mag_coil_types is to change coil type 3022 to 3024 in the MEG channel definition records in the data files specified on the command line As shown in Tables 5 2 and 5 3 the Neuromag Vectorview systems can contain magnetometers with two different coil sizes coil types 3022 and 3023 vs 3024 The systems incorporating coils of type 3024 were intro duced last At some sites the data files have still defined the magnetome ters to be of type 3022 to ensure compatibility with older versions of Neuromag software In the MNE software as well as in the present version of Neurom
140. are deleted After these modifications raw f if is inserted after the remaining part of the file name If the file is split into multiple parts the additional parts will be called lt name gt lt number gt _raw fif Converting eXimia EEG data EEG data from the Nexstim eXimia system can be converted to the fif for mat with help of the mne_eximiaZ2fiff script It creates a Brain Vision vhdr file and calls mne_brain_vision2fiff Usage mne eximia2fiff orignames file file2 where file file2 are eXimia nxe files and the orignames option is passed on to mne_brain_vision2fiff If you want to convert all data files in a directory say mne eximia2fiff nxe Note This script converts raw data files only 9 3 Converting digitization data The mne_convert_dig_data utility converts Polhemus digitization data between different file formats The input formats are fif The standard format used in MNE The digitization data are typically present in the measurement files hpts A text format which is a translation of the fif format data see Section 9 3 1 below elp A text format produced by the Source Signal Imaging Inc software For description of this probe format see http www sourcesignal com formats_probe html The data can be output in fif and hpts formats Only the last command line option specifying an input file will be honored Zero or more output file options can be present on the command line Impor
141. are usually referred to without specifying the leading directories Thus bem msh 7 src fif is used to refer to the file SUBJECTS_ DIR SUBJECT bem msh 7 src fif It is also recommended that the FreeSurfer environment is set up before using the MNE software 3 3 Cortical surface reconstruction with FreeSurfer The first processing stage is the creation of various surface reconstruc tions with FreeSurfer The recommended FreeSurfer workflow is summa rized on the FreeSurfer wiki pages https surfer nmr mgh harvard edu fswiki RecommendedReconstruction Please refer to the FreeSurfer wiki pages https surfer nmr mgh harvard edu fswiki and other FreeSurfer documentation for more information Important Only the latest 4 0 X and later FreeSurfer distributions con tain a version of tkmedit which is compatible with mne_analyze see Section 7 18 3 4 Setting up the anatomical MR images for MRilab If you have the Neuromag software installed the Neuromag MRI viewer MRIlab can be used to access the MRI slice data created by FreeSurfer In addition the Neuromag MRI directories can be used for storing the MEG MRI coordinate transformations created with mne_analyze see Section 7 16 Doring the computation of the forward solution mne_do_forwand_solution searches for the MEG MRI coordinate in the Neuromag MRI directories see Section 3 11 The fif files created by mne_setup_mrit can be loaded into Matlab with the fiff_read_mri func tion
142. ate an rgb output file Files are produced for all picked times as dictated by the pick and integ options W lt name gt Produce w file snapshots This is the stem of the ouput file name The actual name is derived by stripping anything upto and including the last period from the end of lt name gt According to the hemi sphere Lh w or rh w is then appended Files are produced for all picked times as dictated by the pick and integ options Stc lt name gt Produce stc files for either the original subject or the one selected with the morph option These files will contain data only for the decimated locations If morphing is selected appropriate smoothing is mandatory The morphed maps will be decimated with help of a subdivided icosahedron so that the morphed stc files will always contain 10242 vertices These morphed stc files can be easily aver aged together e g in Matlab since they always contain an identical set of vertices norm lt name gt Indicates that a separate w file containing the noise normalization values will be produced The option spm must also be present Nevertheless the movies and stc files output will contain MNE val ues The noise normalization data files will be called lt name gt lt SNR gt Lh w and lt name gt lt SNR gt rh w 6 5 8 Label processing label lt name gt Specifies a label file to process For each label file the values of the computed esti
143. ate frame transformation from the MEG device coordinates to the MEG head coordinates 246 Table 9 4 The fields of the raw data info structure Eo o e sac raw data type 2 or 16 2 byte signed integer 3 4 byte signed integer 4 single precision float All data in the fif file are written in the big endian byte order The raw data are stored sample by sample E Byte location of this buffer in the original fif file First sample of this buffer Since raw data storing can be switched on and off during the acquisition there might be gaps between the end of one buffer and the beginning of the next Number of samples in the buffer Table 9 5 The bufs member of the raw data info structure 9 14 Converting epochs to Matlab format 9 14 1 The utility mne_epochs2mat converts epoch data including all or selected channels from a raw data file to a simple binary file with an associated description file in Matlab mat file format With help of the description file a matlab program can easily read the epoch data from the simple binary file Signal space projection and bandpass filtering can be optionally applied to the raw data prior to saving the epochs Important The MNE Matlab toolbox described in Chapter 10 provides direct access to raw fif files without conversion with mne_epochs2mat first Therefore it is recommended that you use the Matlab toolbox rather than mne_epochs2mat which creates large files occupying disk space un
144. ate the list of unusable channels in a data file see Section 11 4 1 mne_mark_bad_channels Morph label file definitions between subjects see Section 8 5 mne_morph_labels mne_organize_dicom Organized DICOM MRI image files into directories see Section A 2 1 Perform the geometry calculations for BEM forward solu tions see Section 5 7 mne_prepare_bem_model mne_process_stc Manipulate stc files mne_raw2mat Convert raw data into a Matlab file see Section 9 13 mne_rename_channels Change the names and types of channels in a fif file see Section 11 4 5 Compute a sensitivity map and output the result in a w file mne_sensitivity_map see Section 11 10 mne_sensor_locations mne_show_fiff mne_simu Create a file containing the sensor locations in text format List contents of a fif file see Section 11 3 Simulate MEG and EEG data see Section 11 13 mne_smooth Smooth a w or stc file mne_surf2bem Create a fif file describing the triangulated compartment boundaries for the boundary element model BEM see Section 5 6 mne_toggle_skips Change data skip tags in a raw file into ignored skips or vice versa Transform between MRI and MEG head coordinate frames see Section 11 11 mne_transform_points mne_tufts2fiff Convert EEG data from the Tufts University format to fif format see Section 9 2 9 Starts a PDF reader to show this manual from its standard location mne_view_ manual mne_vol
145. atrix is not affected by this option if the source orienta tions are fixed to be normal to the cortical mantle If all three source components are included the forward three source orientations par allel to the coordinate axes is computed If mricoord is present these axes correspond to MRI coordinate system rather than the default MEG head coordinate system This option is useful only in special circumstances meas lt name gt This file is the measurement fif file or an off line average file pro duced thereof It is recommended that the average file is employed for evoked response data and the original raw data file otherwise This file provides the MEG sensor locations and orientations as well as EEG electrode locations as well as the coordinate transformation between the MEG device coordinates and MEG head based coordi nates fwd lt name gt This file will contain the forward solution as well as the coordinate transformations sensor and electrode location information and the source space data A name of the form lt name gt fwd_fif is recom mended meg Compute the MEG forward solution MSH MNE 115 a The forward solution 5 9 3 5 9 4 116 eeg Compute the EEG forward solution grad Include the derivatives of the fields with respect to the dipole posi tion coordinates to the output see Section 5 9 6 Implementation of software gradient compensation As described in Section 9 2 4 the CTF and 4D N
146. box is identical to the one used for evoked responses Figure 7 8 except that data set selector is replaced by the epoch selector show in Figure 7 9 yi Fj j ad et j d Epochs to select Event i Event source lt Data file gt Select Time range from 200 ms to 500 ms Inverse operator 3 sample audvis ave 5 meg eeg iny fit Figure 7 9 The raw data epoch selector The epoch selector contains the following controls 1 The event specifier Only events matching this number are going to be considered 2 The event source specifier The event source can be either the data file i e the digital trigger channel or a event data file produced with mne_browse_raw or mne_process_raw see Section 4 4 10 Using an MSH MNE Interactive analysis A MSH MNE event data file is useful if e g the epochs to be processed epileptic spikes 3 The time range specification This determines the length of the epoch with respect to the selected event Once the settings have been accepted by clicking OK the first matching epoch will be displayed You can switch between epochs using the data set list accessible through Switch to data set in the File menu 7 7 Data displays 7 7 1 The MEG and EEG signals can be viewed in two ways 1 A selection of MEG or EEG channel is shown in a topographical lay out 2 One representative channel can be selected to the Sample channel dis play by clicking on a channel in the top
147. c files morphed to a single subject s cortical surface are used by mne_average_estimates to combine data from different subjects see Section 8 6 If morphing is selected appropriate smoothing must be specified with the smooth option The morphing process can be made faster by precomputing the necessary morphing maps with mne_make_morph_maps see Section 8 4 More information about morphing and averaging can be found in Chapter 8 135 6 The current estimates 136 morphgrade lt number gt Adjusts the number of vertices in the stc files produced when mor phing is in effect By default the number of vertices is 10242 corre sponding to morphgrade value 5 Allowed values are 3 4 5 and 6 corresponding to 642 2562 10242 and 40962 vertices respec tively surface lt surface name gt Name of the surface employed in the visualization The default is inflated curv lt name gt Specify a nonstandard curvature file name The default curvature files are Lh curv and rh curv With this option the names become Lh lt name gt and rh lt name gt patch lt name gt lt angle deg gt Specify the name of a surface patch to be used for visualization instead of the complete cortical surface A complete name of a patch file in the FreeSurface surf directory must be given The name should begin with lh or rh to allow association of the patch with a hemisphere Maximum of two patch options can be in effect one patch for each
148. calization The savehere option was added see Section 4 2 3 The stderr parameter was added to the averaging definition files see Section 4 13 3 Added compatibility with Elekta Neuromag Report Composer cliplab and improved the quality of hardcopies Both in mne_browse_raw and in mne_analyze a non standard default layout can be set on a user by user basis see Section 4 5 6 MSH MNE Release notes D MSH MNE e mne_browse_raw now includes an interactive editor to create derived channels see Section 4 5 4 e The menus in mne_browse_raw were reorganized and an time point specification text field was added e Possibility to keep the old projection items added to the new projection definition dialog e Added cd option e Added filter buttons for raw files and Maxfilter output to the open dialog e Added possibility to create a graph compatible projection to the Save projection dialog e Added possibility to compute a projection operator from epochs speci fied by events e Added the keepsamplemean option to the covariance matrix computa tion files e Added the digtrigmask option e Added Load channel selections item to the File menu e Added new browsing functionality using the mouse wheel or trackball see Section 4 9 1 e Added optional items to the topographical data displays see Section 4 5 2 e Added an event list window see Section 4 10 2 e Added an annotator window see Section 4 10 4 e Keep event
149. ce are outside of the inner skull surface they will be visible indicating that the inner skull surface is obviously inside the inner skull Note that this criterion is more conservative than the one imposed during the computation of the forward solu tion since the source space points are located on the white matter surface rather than on the pial surface This surface can be displayed only if the BEM file is present see Section 7 10 1 Outer skull The outer skull surface This surface can be made transparent This surface can be displayed only if the BEM file is present and contains the outer skull surface see Section 7 10 1 Scalp The scalp surface This surface can be made transparent The dis play of this surface requires that the scalp triangulation file is present see Section 7 10 1 Digitizer data The 3D digitizer data collected before the MEG EEG acquisition These data are loaded from File Load digitizer data The display can be restricted to HPI coil locations and cardinal landmarks with the option The digitizer points are shown as disks whose radius is equal to the distance of the corresponding point from the scalp sur face Points outside the scalp are shown in red and those inside in blue Distinct shades of cold and warm colors are used for the fidu cial landmarks The HPI coils are shown in green Further informa tion on these data and their use in coordinate system alignment is given in Section 7 16 Helmet The
150. chs2mat mne_raw2mat and mne_simu will not work For csh tcsh the corresponding commands are setenv MNE ROOT lt MNE gt setenv MATLAB ROOT lt Matlab gt source MNE ROOT bin mne_ setup For BEM mesh generation using the watershed algorithm or on the basis of multi echo FLASH MRI data see Appendix A and for accessing the tkmedit program from mne_analyze see Section 7 18 the MNE software needs access to a FreeSurfer license and software Therefore to use these features it 1s mandatory that you set up the FreeSurfer environment as described in the FreeSurfer documentation The environment variables relevant to the MNE software are listed in 2 3 MNE_ROOT Location of the MNE software see above FREESURFER HOME Location of the FreeSurfer soft ware Needed during FreeSurfer reconstruction and if the FreeSurfer MRI viewer is used with mne_analyze see Section 7 18 SUBJECTS DIR Location of the MRI data Table 2 3 Environment variables MSH MNE 17 2 Overview SUBJECT Name of the current subject MNE_TRIGGER CH NAME Name of the trigger channel in raw data see Section 4 2 1 MNE_TRIGGER_CH_MASK Mask to be applied to the trigger channel values see Section 4 2 1 Table 2 3 Environment variables Note Appendix B contains information specific to the setup at the Marti nos Center including instructions to access the Neuromag software 18 MSH MNE cHapter3 The Cookbook 3 1 Overview This section describes t
151. column lists the types of the channesl 1 MEG 2 EEG The second column lists the coil types see Tables 5 2 and 5 3 For EEG electrodes this value equals one Logical channel numbers as listed in the fff ile ch_units nchan x 2 Units and unit multipliers as listed in the fif file The unit of the data is listed in the first column T 112 T m 201 V 107 At present the second column will be always zero i e no unit multiplier ch_pos nchan x 12 The location information for each channel The first three values specify the origin of the sensor coordinate system or the location of the elec trode For MEG channels the following nine number specify the x y and z direction unit vectors of the sensor coordinate system For EEG electrodes the first vector after the elec trode location specifies the location of the refer ence electrode If the reference is not specified this value is all zeroes The remaining unit vec tors are irrelevant for EEG electrodes ch_cals nchan x 2 The raw data output by mne_raw2mat is uncali brated The first column is the range member of the fiff data structures and while the second is the cal member To get calibrared data values in the units given in ch_units from the raw data the data must be multiplied with the product of range and cal Table 9 4 The fields of the raw data info structure MSH MNE 245 Data conversion O we O se OOOO mn meg_head_trans The coordin
152. containing source estimates at selected ROIs The input data file can be either a raw data or evoked response MEG EEG file see Section 6 6 Using the MNE Matlab toolbox it is possible to perform many of the above operations in Matlab using your own Matlab code based on the MNE Matlab toolbox For more information on the MNE Matlab tool box see Chapter 10 It is also possible to average the source estimates across subjects as described in Chapter 8 39 Ey The Cookbook 40 MSH MNE CHAPTER 4 MSH MNE 4 1 Processing raw data Overview The raw data processor mne_browse_raw 1s designed for simple raw data viewing and processing operations In addition the program is capable of off line averaging and estimation of covariance matrices mne_browse_raw can be also used to view averaged data in the topo graphical layout Finally mne_browse_raw can communicate with mne_analyze described in Chapter 7 to calculate current estimates from raw data interactively mne_browse_raw has also an alias mne_process_raw If mne_process_raw is invoked no user interface appears Instead com mand line options are used to specify the filtering parameters as well as averaging and covariance matrix estimation command files for batch pro cessing This chapter discusses both mne_browse_raw and mne_process_raw 4 2 Command line options 4 2 1 This section first describes the options common to mne_browse_raw and mne_process_raw There
153. corner frequency projoff Do not apply signal space projection and average electrode refer ence to the data Regardless the projection information is included with the data file so that it can be applied later It is also possible to specify the projon option but then there is no possibility to view the original data in subsequent phases of the analysis 305 12 The sample data set 306 12 9 12 9 1 12 9 2 Saveavetag Specifies how the averages are named With this option the _raw fif ending is stripped of the original raw data file and the tag specified with this option ave is added The average file and the corresponding log file will have the extensions fif and log respectively ave Specifies the averaging script As a result of running the averaging script a file called sample audvis ave fif is created It contains averages to the left and right ear auditory as well as to the left and right visual field stimuli Viewing the off line average The average file computed in the previous section can be viewed in mne_browse_raw To view the averaged signals invoke mne_browse_raw cd SSAMPLE MEG sample mne browse raw amp This Section gives only very basic information about the use of mne_browse_raw for viewing evoked response data Please consult Chapter 4 for more comprehensive information Loading the averages mne_browse_raw loads all the available data from an average file at once 1 Sele
154. cripts have changed The installation and user level effects of the new software organization are discussed in Chapter 2 and Appendix C In addition several minor bugs have been fixed in the source code Most relevant changes visible to the user are listed below D 4 2 Matlab tools e The performance of the fiff I O routines has been significantly improved thanks to the contributions of Fran ois Tadel at USC e Label file I O routines mne_read_label_ file and mne_write_label_file as well as a routine to extract time courses corresponding to a label from an stc file mne_label_time_courses have been added e The patch information is now read from the source space file and included in the source space data structure D 4 3 mne_browse_raw e Rejection criteria to detect flat channels have been added see Sections 4 13 2 and 4 14 2 e Possibility to detect temporal skew between trigger input lines has been added see Sections 4 13 2 and 4 14 2 e allowmaxshield option now works in the batch mode as well 347 D Release notes e Added the projevent option to batch mode e It is now possible to compute an SSP operator for EEG see Section 4 6 4 D 4 4 mne_analyze e Both hemispheres can now be displayed simultaneously see Section 7 8 3 e Ifthe source space was created with mne_make_source_space version 2 3 or later the subject s surface data are automatically loaded after loading the data and the inverse operator
155. ct Open evoked from the File menu 2 Select the average file sample audvis ave fif file from the list and click OK 3 A topographical display of the waveforms with gradiometer channels included appears Inspecting the auditory data Select the left and right ear auditory stimulus responses for display 1 Select Manage averages from the Adjust menu 2 Click off all other conditions except the auditory ones Set the time scale and baseline MSH MNE The sample data set 12 MSH MNE 12 9 3 1 Select Scales from the Adjust menu 2 Switch off Autoscale time range and set the Average time range from 200 to 500 ms 3 Switch on Use average display baseline and set Average display base line from 200 to 0 ms 4 Click OK You can display a subset of responses from the topographical display by holding the shift key down and dragging with the mouse left button down When you drag on the response with just the left button down the signal timing and channel name are displayed at the bottom If the left mouse button is down and you press shift down the time is give both in absolute units and relative to the point where shift was pressed down Observe the following 1 The main deflection occurs around 100 ms over the left and right tem poral areas 2 The left ear response shown in yellow is stronger on the right than on the left The opposite is true for the right ear response shown in red Inspecting the v
156. ctories named lt three digit gt number corresponding to one or more subsets of images in this series protocol The only subset division scheme implemented in mne_organize_dicom 1s that according to differ ent echoes typically found in multi echo FLASH data These second level directories will contain symbolic links pointing to the original image data Note mne_organize_dicom was developed specifically for Siemens DICOM data Its correct behavior with DICOM files originating from other MRI scanners has not been verified at this time Tip Since mne_organize_dicom processes all images not only the FLASH data it may be a useful preprocessing step before FreeSurfer reconstruction process as well A 2 2 Creating the surface tessellations The BEM surface segmentation and tessellation is automated with the script mne_flash_bem It assumes that a FreeSurfer reconstruction for this subject is already in place To run this utility 1 Run mne_organize_dicom as described above 2 Change to the lt dest gt directory where mne_organize_dicom created the image directory structure 3 Create symbolic links from the directories containing the 5 degree and 30 degree FLASH series to flash05 and flash30 respectively e in s lt FLASH 5 series dir gt lash05 e in s lt FLASH 30 series dir gt lash30 4 Set the SUBJECTS DIR and SUBJECT environment variables 5 Run mne_flash_bem It may take a while for mne_flash_bem to complete It uses th
157. d fmax option is not specified F pax Pmiq t 17 F max slope 137 6 The current estimates 138 6 5 7 Output files mov lt name gt Produce QuickTime movie files This is the stem of the ouput file name The actual name is derived by stripping anything upto and including the last period from the end of lt name gt According to the hemisphere 1h or rh is then appended The name of the view is indicated with lt viename gt Finally mov is added to indicate a QuickTime output file The movie is produced for all times as dic tated by the tmin tmax tstep and integ options qual lt value gt Quality of the QuickTime movie output The default quality is 80 and allowed range is 25 100 The size of the movie files is a monotonously increasing function of the movie quality rate lt rate gt Specifies the frame rate of the QuickTime movies The default value is 1 7 CIOT ten where Len is the time between subsequent movie frames produced in seconds rgb lt name gt Produce rgb snapshots This is the stem of the ouput file name The actual name is derived by stripping anything upto and including the last period from the end of lt name gt According to the hemi sphere 1h or rh is then appended The name of the view is indi cated with lt viename gt Finally rgb is added to indicate an rgb output file Files are produced for all picked times as dictated by the pick
158. d click Show points on the surface displayed in the vicinity of the dipoles will be painted according to the specifications given in the Options section of the dialog Color By the default the dipoles are marked in green with transparency alpha set to 0 5 I you click on one of the dipoles you can adjust the color of this dipole by editing the color values or from the color editor appearing when you click Color When you click Apply the new color values are attached to the selected dipole Max distance for dipoles to show mm If this option is on only dipoles which are closer to the surface than the distance specified in the adjacent text field are displayed Paint all point closer than mm Instead of indicating the point closest to the dipole all points closer than the distance given in the text field will be painted if this option is on This choice is useful for understanding the shape of the neigh borhood of a dipole on the cortical surface Number of smooth steps This option spreads out the dipole marking by the given number of smooth steps to make the dipoles more clearly visible A suitable choice is 3 or 4 191 Ea Interactive analysis Keep previous dipoles If this option is on previously marked dipoles are not cleared from the display before new ones are shown Note The surface must be loaded to display dipole locations To calculate the distance from the dipoles to the white matter surface the white matter
159. d as the one applying to raw data To reflect the decrease of noise due to averaging this matrix Cy is scaled by the number of averages L i e C C L As shown above regularization of the inverse solution is equivalent to a change in the variance of the current amplitudes in the Bayesian a priori distribution Convenient hoice for ny source covariance matrix R is such that trace GRG trace I 1 With this choice we can approximate ae SNR where SNR is a power signal to noise ratio of the whit ened data Note The definition of the signal to noise ratio a relationship given above works nicely for the whitened forward solution In the un whitened case scaling with the trace ratio trace GRG y trace C does not make sense since the diagonal elements summed have in general different units of measure For example the MEG data are expressed in T or T m whereas the unit of EEG is Volts Regularization of the noise covariance matrix Since finite amount of data is usually available to compute an estimate of the noise covariance matrix C the smallest eigenvalues of its estimate are usually inaccurate and smaller than the true eigenvalues Depending on the seriousness of this problem the following quantities can be affected 1 The model data predicted by the current estimate 2 Estimates of signal to noise ratios which lead to estimates of the required regularization see Section 6 2 2 3 The estimated current values
160. d in the interactive version of the program The default is 40 Hz lowpassw lt value Hz gt The width of the transition band of the lowpass filter This value can be adjusted in the interactive version of the program The default 1s 5 Hz MSH MNE Data conversion 9 MSH MNE 9 14 2 9 14 3 filteroff Do not filter the data proj lt name gt Include signal space projection SSP information from this file If the inv option is present proj has no effect Note Baseline has not been subtracted from the epochs This has to be done in subsequent processing with Matlab if so desired Note Strictly speaking trigger mask value zero would mean that all trig ger inputs are ignored However for convenience setting the mask to zero or not setting it at all has the same effect as OXFFFFFFFF i e all bits set Tip The digital trigger channel can also be set with the MNE_TRIGGER CH NAME environment variable Underscores in the variable value will not be replaced with spaces by mne_browse_raw or mne_process_raw Using the digtrig option supersedes the MNE_TRIGGER CH NAME environment variable Tip The digital trigger channel mask can also be set with the MNE_TRIGGER_CH_MASK_ environment variable Using the digtrigmask option supersedes the MNE_ TRIGGER _CH_MASK environment variable The binary epoch data file mne_epochs2mat saves the epoch data extracted from the raw data file is a simple binary file The data ar
161. d surface triangulation Tip Different methods can be employed for the creation of the individual surfaces For example it may turn out that the watershed algorithm pro duces are better quality skin surface than the segmentation approach based on the FLASH images If this is the case outer _skin surf can set to point to the corresponding watershed output file while the other sur faces can be picked from the FLASH segmentation data Tip The triangulation files can include name of the subject as a prefix lt subject name gt e g duck inner skull surf Tip The mne_convert_surface utility described in Section 9 7 can be used to convert text format triangulation files into the FreeSurfer surface format Important Aliases created with the Mac OSX finder are not equivalent to symbolic links and do not work as such for the UNIX shells and MNE programs 3 7 Setting up the boundary element model This stage sets up the subject dependent data for computing the forward solutions 1 The fif format boundary element model geometry file is created This step also checks that the input surfaces are complete and that they are topologically correct i e that the surfaces do not intersect and that the surfaces are correctly ordered outer skull surface inside the scalp and inner skull surface inside the outer skull Furthermore the range of tri angle sizes on each surface is reported For the three layer model the minimum distance betwe
162. ding surface By default there will be no exclu sion mri lt name gt Specifies a MRI volume in mgz or mgh format If this argument is present the output source space file will contain a sparse interpola tion matrix which allows mne_volume_data2mri to create an MRI overlay file see Section 9 4 pos lt name gt Specifies a name of a text file containing the source locations and optionally orientations Each line of the file should contain 3 or 6 values If the number of values is 3 they indicate the source loca tion in millimeters The orientation of the sources will be set to the z direction If the number of values is 6 the source orientation will be parallel to the vector defined by the remaining 3 numbers on each line With pos all of the options defined above will be ignored By default the source position and orientation data are assumed to be given in MRI coordinates head If this option is present the source locations and orientations in the file specified with the pos option are assumed to be given in the MEG head coordinates meters Indicates that the source locations in the file defined with the pos option are give in meters instead of millimeters 100 MSH MNE The forward solution a MSH MNE Src lt name gt Specifies the output file name Use a name lt dir gt lt name gt src fif all Include all vertices in the output file not just those in use This option is implied w
163. directory was added to several file loading dialogs The vertex coordinates can now be displayed see Section 7 8 4 D 3 3 3 mne_average_forward_solutions EEG forward solutions are now averaged as well see Section 5 10 D 3 3 4 mne_browse_raw and mne_process_raw Improvements in the raw data processor mne_browse_raw mne_process_raw include The name of the digital trigger channel can be specified with the MNE_TRIGGER CH NAME environment variable The format of the text event files was slightly changed The sample numbers are now absolute sample numbers taking into account the initial skip in the event files The new format is indicated by an addi tional pseudoevent in the beginning of the file mne_browse_raw and mne_process_raw are still compatible with the old event file format For details see Section 4 10 5 Using information from the fif data files the wall clock time corre sponding to the current file position is shown on the status line mne_browse_raw can now control mne_analyze to facilitate interactive analysis of clinical data If the length of an output raw data file exceeds the 2 Gbyte fif file size limit the output is split into multiple files split and events options was added to mne_process_raw The allowmaxshield option was added to mne_browse_raw to allow loading of unprocessed data with MaxShield in the Elekta Neu romag systems These kind of data should never be used as an input for source lo
164. e fmrioff option It turns out that the MRI weighting has a strong influence on the MNE but the noise normalized estimates are much less affected by it 127 6 The current estimates 6 3 Effective number of averages It is often the case that the epoch to be analyzed is a linear combination over conditions rather than one of the original averages computed As stated above the noise covariance matrix computed is originally one cor responding to raw data Therefore it has to be scaled correctly to corre spond to the actual or effective number of epochs in the condition to be analyzed In general we have C Co L ore where Ls 1s the effective number of averages To calculate Lie for an arbitrary linear combination of conditions y t W x t l we make use of the the fact that the noise covariance matrix n n 2 C X wre Co w7 L i l lal which leads to n 2 I Lege X w7 L i An important special case of the above is a weighted average where n w L gt Li Isl and therefore n Leg gt Li Lel 128 MSH MNE The current estimates ol MSH MNE Instead of a weighted average one often computes a weighted sum a sim plest case being a difference or sum of two categories For a difference w l and w l and thus L Loge 1 L 1 L Or O hilg CIRT 1 49 Interestingly the same holds fora sum where w w 1 General izing for any combination of sums and diffe
165. e and median sensor movements are listed The graphical display contains the following data 1 The geometric mean of the HPI coil goodness of fits red curve The scale for this curve is always 0 9 1 0 2 The average coil sensor movement value blue curve The scale is adjustable from the buttons below the display 3 The estimated angular velocity deg s green curve The scale is adjustable from the buttons below the display 4 The current time point indicated with a black cursor The slider below the display can be used to select the time point If you click on the slider the current time can be adjusted with the arrow keys 197 Ea Interactive analysis 198 The current head position with respect to the sensor array is show in the viewer window if it is visible see Section 7 10 Note that a complete set of items listed above is only available if a data file has been previously loaded see Section 7 5 7 18 Working with the MRI viewer 1 TX MRI viewer control Display options O Show MRI viewer user interface O Track surface location in MIRI J Show dipole locations in WIRI JO Show digitizer data in MRI J Interpolate voxels J Max intensity projection O Show segmentation data in MRI Recenter MRI display snow surface data in WIRI M show command input and output A ml za F Figure 7 30 The MRI viewer control window Selecting Show MRI viewer from the View menu starts the FreeSu
166. e EEG eigenvectors as well as the existing projection items is displayed MSH MNE Processing raw data 4 MSH MNE Using the projection selector you can experiment which vectors have a significant effect on the noise level of the data You should strive for using a minimal number of vectors When the selection is complete you can click Accept to introduce this selection of vectors as the new projection operator Discard abandons the set of calculated vectors Whenever EEG channels are present in the data a projection item corresponding to the average EEG reference is automatically added when a new projection operator is introduced More information on the SSP method can be found in Section 4 16 Note The new projection data created in mne_browse_raw 1s not auto matically copied to the data file You need to create a standalone projec tion file from File Save projection to save the new projection data and load it manually after the data file has been loaded if you want to include in any subsequent analysis Tip The command line options for mne_process_raw allow calculation of the SSP operator from continuous data in the batch mode see Section 4 2 3 4 7 The Windows menu show full view show averages show event list show annotator Manage averages start mne_analyze Quit mne_analyze Figure 4 12 The Windows menu The Windows menu shown in Figure 4 12 contains the following items Show full view Brings
167. e FreeSurfer directory structure under SSUBJECTS DIR SSUBJECT The script encapsulates the following processing steps 1 It creates an mgz file corresponding to each of the eight echoes in each of the FLASH sequences in mri flash The files will be called mef lt flip angle gt _ lt echo number gt mgz 2 It creates parameter maps in mri flash parameter maps using mri_ms_fitparms 3 It creates a synthetic 5 degree flip angle volume in mri flash parameter maps flash5 mgz using mri_synthesize 4 Using fsl_rigid_register it creates a registered 5 degree flip angle vol ume mri flash parameter maps flash5 reg mgz by reg istering mri flash parameter maps flash5 mgz to the T volume under mri 321 A Creating the BEM meshes 322 5 Using mri_convert it converts the flash5_reg volume to COR format under mri flash5 If necessary the T and brain volumes are also converted into the COR format 6 It runs mri_make_bem_surfaces to create the BEM surface tessella tions 7 It creates the directory bem flash moves the tri format tringulations there and creates the corresponding FreeSurfer surface files in the same directory 8 The COR format volumes created by mne_flash_bem are removed A 2 3 Inspecting the meshes It is advisable to check the validity of the BEM meshes before using them This can be done with help of tkmedit either before or after executing mne_setup_forward_model see Section 3 7 A 3 Using seglab The brai
168. e applied to the data from File Save bad channel selection Middle button click or drag with control key Extends the bad channel selection without clearing the previously active bad channels Right button Adjusts the channel selection used for dipole fitting in the same way as the middle button selects bad channels For more information on channel selections see Section 7 15 4 The sample channel display The sample channel display shows one of the measurement channels at the upper left corner of the mne_analyze user interface A time point can be selected with a left mouse click In addition the following keyboard functions are associated with the sample channel display Down Change the sample channel to the next channel in the scanning order Up Change the sample channel to the previous channel in the scanning order Right Move forward in time by 1 ms Control Right Move forward in time by 5 ms Left Move backward in time by 1 ms Control Left Move backward in time by 5 ms Scale settings The scales of the topographical and sample channel display can be adjusted from the Scales dialog which is invoked by selecting Adjust MSH MNE Interactive analysis A Scales from the menus The Scales dialog shown in Figure 7 10 has the following entries Analyze range min ms Specifies the lower limit of the time range of data to be shown Analyze range max ms Specifies the upper limit of the time range of data t
169. e first k left singular vectors of I The weights of the regularized estimate are T where AS 1S diagonal with JJ AP a JSP otherwise A being the singular value of I The truncation point p is selected in mne_analyze by specifying a tolerance which is used to determine p such that MSH MNE Interactive analysis ZA MSH MNE va ji Zl lt e X The extrapolated and interpolated magnetic field or potential distribution estimates x in a virtual grid of sensors can be now easily computed from the regularized minimum norm estimate With LiL j are the lead fields of the virtual sensors x Dw pe 7 11 3 Field mapping preferences The parameters of the field maps can be adjusted from the Field mapping preferences dialog shown in Figure 7 20 which is accessed through the Adjust Field mapping menu item ean wX Field mapping preferences MEG SVD truncation at 0000 PMaeiseipy te rha npieifes Ss X Re MARAT EEG SVD truncation at 0000 PMaeiseipy te rha npieifes DES ETE E X Re MALAT A E E ge cei tees t PN bas TEE H See a Kr MARA PMaeisaipy sa pHs EEEREN KA yi a ir MALAT AE PAsdeaiys cv Iraga riny oe ey oe Ga oe gy a Ainii Se KARAT ne Bat ean Ses oe W se default origin W Use default origin net gtiyagiga SS KRAAM Downsampling grade A T ome Go N A E AE Sed a E S a Number of smoothsteps J Extrapolate to scalp MEG contour s
170. e names to be modi fied MSH MNE Miscellaneous utilities 11 MSH MNE 11 4 2 11 4 3 Fixing the encoding of the trigger channel mne_fix_stim14 Some earlier versions of the Neuromag acquisition software had a prob lem with the encoding of the eighth bit on the digital stimulus channel STI 014 This problem has been now fixed Old data files can be fixed with mne_fix_stiml4 which takes raw data file names as arguments mne_fix_stiml4 also changes the calibration of STI 014 to unity If the encoding of STI 014 is already correct running mne_fix_stiml4 will not have any effect on the raw data In newer Neuromag Vectorview systems with 16 bit digital inputs the upper two bytes of the samples may be incorrectly set when stimulus input 16 is used and the data are acquired in the 32 bit mode This prob lem can be fixed by running mne_fix_stim 4 on a raw data file with the 32 option mne fix stiml4 32 lt raw data file gt In this case the correction will be applied to the stimulus channels STI101 and STI201 Updating EEG location info mne_check_eeg_locations Some versions of the Neuromag acquisition software did not copy the EEG channel location information properly from the Polhemus digitizer information data block to the EEG channel information records if the number of EEG channels exceeds 60 The purpose of mne_check_eeg_locations is to detect this problem and fix it if requested The command line options
171. e number 1 i e all magnetometer channels MEG 2 3 Selects all MEG gradiometer channels EEG STI 014 Selects all EEG channels and stimulus channel STI 014 M Selects all channels whose names begin with the letter M Table 4 1 Examples of regular expressions for channel selections Note The interactive tool for creating the channel selections does not allow you to change the order of the selected channels from that given by the list of channels However the ordering can be easily changed by man ually editing the channel selection file in a text editor 4 5 6 Full view layout Shows a selection of available layouts for the topographical views full view and average display The system wide layout files reside in SMNE ROOT sShare mne mne analyze lout In addition any lay MSH MNE 61 4 Processing raw data 62 4 5 7 out files residing in SHOME mne 1lout are listed The default layout is Vectorview grad If there is a layout file in the user s private layout direc tory ending with default lout that layout will be used as the default instead The Default button returns to the default layout The format of the layout files 1s lt plot area limits gt lt viewport definition 1 gt lt viewport definition N gt The lt plot area limits gt define the size of the plot area Xinin Xmax min Vmax Which should accommodate all view ports When the layout is used the plot area will preserve its aspect ratio
172. e of the data will be taken and the neg ative sign will be transferred to the result unless abs is specified Valid in all contexts Rules of application are identical to abs sqrt Means pow 0 5 The effects of the options can be summarized as follows Suppose that the description file includes P contexts and the temporally resampled data are organized in matrices S where p 1 P is the subject index and the rows are the signals at different vertices of the cortical surface The aver age computed by mne_average_estimates is then Ol with Bp p r _ a By wp sen Sie p 1 and r Wp W gt Wol p 1 In the above B and w are the powers and weights assigned to each of the subjects whereas B and w are the output weight and power value respectively The sign is either included a 1 1 or omitted OL 2 amp 2 depending on the presence of abs phrases in the description file Note mne_average_estimates requires that the number of vertices in the Stc files are the same and that the vertex numbers are identical This will be the case if the files have been produced in mne_make_movie using the morph option Note It is straightforward to read and write stc files using the MNE Mat lab toolbox described in Chapter 10 and thus write custom Matlab func tions to realize more complicated custom group analysis tools MSH MNE CHAPTER 9 MSH MNE 9 1 Data conversion Overvi
173. e option here default 1000 Hz tmin lt time ms gt Explain the option here default 200 ms tmax lt time ms gt Explain the option here default 500 ms seed lt number gt Specifies the seed for random numbers This seed is used both for adding noise see Section 11 13 3 and for random numbers in source waveform expressions see Section 11 13 5 If no seed is specified the current time in seconds since Epoch January 1 1970 is used all Activate all sources on the cortical surface uniformly This overrides the label1 options Noise simulation Noise is added to the signals if the Senscov and nave options are present If nave is omitted the number of averages is set to L 100 The noise is computed by first generating vectors of Gaussian random numbers n ft with n At N O 1 Thereafter the noise covariance matrix Cis used to color the noise MSH MNE Miscellaneous utilities 11 n t AU aO where we have used the eigenvalue decomposition positive definite cova riance matrix C UA U Note that it is assumed that the noise covariance matrix is given for raw data i e for L 1 11 13 4 Simulated data The default source waveform q for the k label is nonzero at times tin 100 k 1 p f p 0 100 with 2 T TT Tay Q COs z2 7 1 e the source waveforms are non overlapping 100 samples wide cos pulses The sampling frequency f 600Hz The source amplitude Q i
174. e selection dialog to select the noise covariance matrix file An existing selection can be cleared with the Unset button Omit off diagonal terms If a noise covariance matrix is selected this choice omits the off diagonal terms from it This means that individual noise estimates for each channel are used but correlations among channels are not taken into account Regularization Regularize the noise covariance before using it in whitening by add ing a multiple of an identity matrix to the diagonal This is discussed in more detail in Section 6 2 4 Especially if EEG is included in fit ting it is advisable to enter a non zero value around 0 1 here Planar fixed fT cm In the absense of a noise covariance matrix selection a diagonal noise covariance with fixed values on the diagonal is used This entry specifies the fixed value of the planar gradiometers 187 Ea Interactive analysis Axial fixed fT If a noise covariance matrix file is not specified this entry specifies a fixed diagonal noise covariance matrix value for axial gradiome ters and magnetometers EEG fixed u V If a noise covariance matrix file is not specified this entry specifies a fixed diagonal noise covariance matrix value for axial gradiome ters and magnetometers O X Dipole fitting preferences Forward model Sphere origin x mm 10 0 Sphere origin y mm 0 0 Sphere origin z mm 140 0 EEG scalp radius mm 90 0 EEG sphere m
175. e space information into text files suitable for loading into the Neuromag MRIlab software The command line options are version Show the program version and compilation date help List the command line options src lt name gt The source space to be listed This can be either the output from mne_make_source_space src fif output from the forward calcu lation fwd fif or the output from the inverse operator decompo sition inv fif mri lt name gt A file containing the transformation between the head and MRI coordinates is specified with this option This file can be either a Neuromag MRI description file the output from the forward calcu lation fwd fif or the output from the inverse operator decompo sition inv fif If this file is included the output will be in head coordinates Otherwise the source space will be listed in MRI coor dinates dip lt name gt Specifies the stem for the Neuromag text format dipole files to be output Two files will be produced lt stem gt lh dip and lt stem gt rh dip These correspond to the left and right hemisphere part of the source space respectively This source space data can be imported to MRIIab through the File Import Dipoles menu item MSH MNE 229 9 Data conversion 230 pnt lt name gt Specifies the stem for Neuromag text format point files to be out put Two files will be produced lt stem gt lh pnt and lt stem gt rh p
176. e stored as big endian single precision float ing point numbers Assuming that each of the total of p epochs contains n channels and m time points the data s ik ar e ordered as 51111718211 mn1 mnp 9 where the first index stands for the time point the second for the channel and the third for the epoch number respectively The data are not cali brated 1 e the calibration factors present in the Matlab description file have to be applied to get to physical units as described below Note The maximum size of an epoch data file is 2 Gbytes 7 e 0 5 Gsam ples Matlab data structures The Matlab description files output by mne_epochs2mat contain a data structure lt tag gt _epoch_info The fields of the this structure are listed in 249 9 Data conversion Table 9 4 Further explanation of the epochs member is provided in Table 9 7 O vwe se ewan orig_file string The name of the original fif file specified with the raw option epoch_file string The name of the epoch data file produced by mne_epocs2mat epochs nepoch x 5 Description of the content of the epoch data file see Table a ls highpass Highpass filter frequency Hz ch_names nchan string String array containing the names of the chan nels included ch_types nchan x 2 The column lists the types of the channels 1 MEG 2 EEG The second column lists the coil types see Tables 5 2 and 5 3 For EEG electrodes this value equals one Logical channe
177. e_browse_raw and mne_process_raw see Chapter 4 In addition in the mapping between TAL labels and trig ger numbers provided by the annotmap option is employed to assign trigger numbers in the event file produced In the absense of the annotmap option default trigger number 1024 is used annotmap lt filename gt Specify a file which maps the labels of the TALs to numbers on a trigger channel STI 014 which will be added to the output file if this option is present This annotation map file may contain com ment lines starting with the or characters The data lines contain a label number pair separated by a colon For example a MSH MNE Data conversion 9 MSH MNE line Trigger 1 9 means that each annotation labeled with the text Trigger 1 will be translated to the number 9 on the trigger channel elp lt filename gt Specifies the name of the an electrode location file This file is in the probe file format used by the Source Signal Imaging Inc soft ware For description of the format see http www sourcesig nal com formats_probe html Note that some other software packages may produce electrode position files with the elp ending not conforming to the above specification As discussed above the fiducial marker locations optional in the probe file format specifi cation are mandatory for mne_edf2fiff When this option 1s encoun tered on the command line any previously specified
178. e_data and mne_compute_mne no longer have command line options to restrict the time range of evoked data input mne_change_ baselines It is now possible to process all data sets in a file at once All processed data are stored in a single output file New utilities D 2 13 1 mne_show_fiff Replacement for the Neuromag utility show_fiff This utility conforms to the standard command line option conventions in MNE software For details see Section 11 3 D 2 13 2 mne_make_cor_set Replaces the functionality of the Neuromag utility create_mri_set_simple to create a fif format description file for the FreeSurfer MRI data This utility is called by the mne_setup_mri script 339 D Release notes 340 D 2 14 D 2 15 D 2 13 3 mne_compensate_data This utility applies or removes CTF software gradient compensation from evoked response data see Section 9 2 4 D 2 13 4 mne_insert_4D_comp This utility merges 4D Magnes compensation data from a text file and the main helmet sensor data from a fif file and creates a new fif file Section 9 2 5 D 2 13 5 mne_ctf_dig2fiff This utility reads a text format Polhemus data file transforms the data into the Neuromag head coordinate system and outputs the data in fif or hpts format D 2 13 6 mne_kit2fiff The purpose of this new utility is to import data from the KIT MEG sys tem see Section 9 2 7 D 2 13 7 mne_make_derivations This new utility will take derivation data from a text file and
179. e_fix_stiml4 Fix coding errors of trigger channel STI 014 see Section 3 9 1 mne_flash_bem Create BEM tessellation using multi echo FLASH MRI data see Section A 2 Read Magnes compensation channel data from a text file and merge it with raw data from other channels in a fif file see Section 9 2 5 mne_list_bem List BEM information in text format see Section 9 6 mne_list_coil_def Create the coil description file This is run automatically at when the software is set up see Section 5 8 5 mne_list_proj List signal space projection data from a fif file mne_list_source_space List source space information in text format suitable for importing into Neuromag MRIIab software see Section 9 5 mne_list_versions List versions and compilation dates of MNE software mod ules see Section 11 2 mne_make_cor_set Used by mne_setup_mri to create fif format MRI descrip tion files from COR or mgh mgz format MRI data see Section 3 4 The mne_make_cor_set utility is described in Section 9 8 Create a channel derivation data file see Section 11 5 mne_make_eeg_layout Make a topographical trace layout file using the EEG elec trode locations from an actual measurement see Section 11 6 mne_make_morph_maps Precompute the mapping data needed for morphing between subjects see Section 8 4 Create a spatially uniform stc file for testing purposes Table 2 2 Utility programs 14 MSH MNE Overview Purpose Upd
180. ead coordinates see Section 5 3 EKG scalp radius mm Specifies the radius of the outermost shell in the EEG sphere model For details see Section 5 9 4 MSH MNE Interactive analysis 7 MSH MNE EEG sphere model name Specifies the name of the EEG sphere model to use For details see Section 5 9 4 BEM model Selects the boundary element model to use The button labeled with brings up a file selection dialog to select the BEM file An exist ing selection can be cleared with the Unset button If EEG data are included in fitting this must be a three compartment model Note that the sphere model is used even with a BEM model in effect see Section 7 15 2 Accurate field calculation Switches on the more accurate geometry definition of MEG coils see Section 5 8 In dipole fitting there is very little difference between the accurate and normal coil geometry definitions The Modalities section defines which kind of data MEG EEG are used in fitting If an inverse operator is loaded with the data this section is fixed and greyed out You can further restrict the selection of channels used in dipole fitting with help of channel selections discussed in Section 7 15 4 The Noise estimate section of the dialog contains the following items Noise covariance Selects the file containing the noise covariance matrix If an inverse operator is loaded the default is the inverse operator file The button labeled with brings up a fil
181. easily by manually edit ing one of the files exported by the KIT system 3 A sensor data file sns file containing the locations and orientations of the sensors This file can be exported directly from the KIT system Note The output fif file will use the Neuromag head coordinate system convention see Section 5 3 A coordinate transformation between the CTF 4D head coordinates and the Neuromag head coordinates is included This transformation can be read with MNE Matlab Toolbox rou tines see Chapter 10 The following input files are optional 1 A head shape data file Asp file containing locations of additional points from the head surface These points must be given in the same coordinate system as that used for the elp file and the fiducial locations must be within 1 mm from those in the elp file 2 A raw data file containing the raw data values sample by sample as text If this file is not specified the output fif file will only contain the measurement info block By default mne_kit2fiff includes the first 157 channels assumed to be the MEG channels in the output file The compensation channel data are not converted by default but can be added together with other channels with the type The channels from 160 onwards are designated as miscella neous input channels MISC 001 MISC 002 etc The channel names and types of these channels can be afterwards changed with the mne_rename_channels utility see Section 11 4 5 In
182. east squares error criterion The optimal dipole amplitude parameters are determined for the opti mal dipole location obtained in steps 2 and 3 The dipole parameters are reported in the dipole list discussed in Section 7 15 3 Additional notes 1 The noise covariance matrix is always applied to the data and the for ward solution as appropriate to correctly weight the different types of MEG channels and EEG Depending on the dipole fitting settings the 189 A Interactive analysis noise covariance may be either a diagonal matrix or a full matrix including the correlations 2 Using the SVD of the whitened gain matrix of three dipole componets at a given location the component producing the weakest signal ampli tude is omitted if the ratio of the smallest and largest singular values is less than 0 2 3 The present MNE software package also contains a batch mode dipole fitting program called mne_dipole_fit This piece of software is not yet documented here However mne dipole fit help lists the command line options which have direct correspondence to the inter active dipole fitting options discussed here 7 15 3 The dipole list Dipole sources List of Sources time ms x mm mm QOx nam Qy n am Qz nim g E 00 6 52 9 17 0 29 1 Saksa aema filea BESE a a 4 6 aama a aa Display options _ Max distance for dipoles to show mm _ Paint all points closer than mm J Number of smooth ste
183. echnical details of the patch information please consult Section 6 2 8 This option is considered experimental at the moment Inv lt name gt Save the inverse operator decomposition here Producing movies and snapshots mne_make_movie is a program for producing movies and snapshot graph ics frames without any graphics output to the screen In addition mne_make_movie can produce stc or w files which contain the numerical MSH MNE The current estimates Lo 6 5 1 6 5 2 6 5 3 MSH MNE current estimate data in a simple binary format for postprocessing These files can be displayed in mne_analyze see Chapter 7 utilized in the cross subject averaging process see Chapter 8 and read into Matlab using the MNE Matlab toolbox see Chapter 10 The command line options to mne_make_movie are explained in the fol lowing subsections General options version Show the program version and compilation date help List the command line options Input files Inv lt name gt Load the inverse operator decomposition from here meas lt name gt Load the MEG or EEG data from this file set lt number gt The data set condition number to load This is the sequential num ber of the condition You can easily see the association by looking at the condition list in mne_analyze when you load the file Stcin lt name gt Specifies an stc file to read as input Times and baseline tmin lt time ms gt Spec
184. ecify this option However for compatibility with previous MNE releases keepsamplemean is not on by default 4 14 3 Covariance definitions The covariance definitions starting with def specify the epochs to be included in the estimation of the covariance matrix event lt number gt The zero time point of an epoch to be averaged is defined by a tran sition from zero to this number on the digital trigger channel The interpretation of the values on the trigger channel can be further modified by the ignore keyword If the event parameter is missing or set to zero the covariance matrix is computed over a section of the raw data defined by the tmin and tmax parameters ignore lt number If this parameter is specified the selected bits on trigger channel val ues can be mask set to zero out prior to checking for an existence of an event For example to ignore the values of trigger input lines three and eight specify ignore 132 2 2 132 delay lt time s gt Adds a delay to the time of the occurrence of an event Therefore if this parameter is positive the zero time point of the epoch will be MSH MNE 83 4 Processing raw data 84 later than the time of the event and correspondingly if the parame ter is negative the zero time point of the epoch will be earlier than the time of the event By default there will be no delay tmin lt time s gt Beginning time point of the epoch If the event parameter is zero or mi
185. ect sample audvis ave fif as your data file and select the Left auditory data set Select the inverse operator sample audvis ave oct 6 meg eeg inv fif and press OK After a while the signals appear in the sample waveform and topographi cal displays Click on the N100m peak in the auditory response A dSPM map appears in the main surface display Show field and potential maps Select Windows Show viewer After a while the viewer window appears Click on the N100m peak again Once the field map preparation computa tions are complete the magnetic field and potential maps appear Investi gate the viewer window options with help of Section 7 10 MSH MNE The sample data set 12 MSH MNE 12 14 5 12 14 6 12 14 7 Show current estimates The options affecting the current estimates are accessible from Adjust Estimate parameters With help of Section 7 12 investigate the effects of the parameter settings Labels and timecourses While in directory MEG sample create a directory called label mkdir label Using the information in Section 7 13 4 create two labels A 1h label and A rh label in the approximate location of the left and right audi tory cortices Save these labels in the newly created Label directory Load all labels from the label directory and investigate the timecourses in these two labels as well as at invidual vertices Information on label processing can be found from Section 7 13 Morphing Goto to
186. ed indent lt number gt Number of spaces for indentation for each deeper level in the tree structure of the fif files The default indentation is 3 spaces in terse and no spaces in verbose listing mode long List all data from string tags instead of the first 80 characters This options has no effect unless the verbose option is also present tag lt number gt List only tags of this kind Multiple tag options can be specified to list several different kinds of data mne_show_fiff reads the explanations of tag kinds block kinds and units from SMNE_ROOT share mne fiff explanations txt 11 4 Data file modification utilities 11 4 1 This section contains utilities which can be used to add information or fix existing information in MEG EFEG data fif files Unless otherwise noted these utilities can be applied to both raw and evoked data files Designating bad channels mne_mark_bad_channels This utility adds or replaces information about unusable bad channels The command line options are version Show the program version and compilation date help List the command line options bad lt filename gt Specify a text file containing the names of the bad channels one channel name per line The names of the channels in this file must match those in the data file exactly If this option is missing the bad channel information is cleared lt data file name gt The remaining arguments are taken as data fil
187. ed BEM surface segmentation data com puted with the watershed algorithm bem inner_skull surf Inner skull surface for BEM bem outer_skull surf Outer skull surface for BEM Table 12 3 Overview of the contents of the subjects sample directory 301 12 The sample data set bem outer_skin surf Skin surface for BEM sample head fif Skin surface in fif format for mne_analyze visualizations 302 12 5 12 5 1 12 5 2 surf Surface reconstructions mri T1 The T1 weighted MRI data employed in visualizations Table 12 3 Overview of the contents of the subjects sample directory The following preprocessing steps have been already accomplished in the sample data set 1 The MRI surface reconstructions have been computed using the Free Surfer software 2 The BEM surfaces have been created with the watershed algorithm see Section A 1 3 The MEG EEG raw data file has been checked with the utilities described in Sections 3 9 1 and 3 9 2 4 Template scripts for averaging and computation of the noise covari ance matrices have been written Setting up subject specific data Structural MRIs To set up the structural MRIs for processing with the Neuromag MRI viewer MRIlab say mne setup mri This command sets up the directories subjects sample mri T1l neuromag and subjects sample mri brain neuromag For more information see Section 3 4 Source space The source space with a 5 mm grid spacing is set up by sayin
188. ed averaging preferences will be applied in the covari ance matrix calculation see Section 4 5 9 Instead of using continuous raw data it is also possible to employ short epochs around triggers events in the calculation of the new SSP operator by specifying a positive event number in the time specification dialog This option is very useful e g to remove MCG ECG artifacts from the data to facilitate detection of epileptic spikes 1 Select left or right temporal channels to the display 2 Mark several peaks of the MCG signal in the data click on the first one and control click on the subsequent ones to extend the selection 3 Select an event number next to the Picked to button in the tool bar see Section 4 11 and click Picked to As a result the lines marking the events will change color by default from green to blue indicating transition to user created events 4 Specify an epoch time range to be employed and the event number selected in the previous step for the SSP operator calculation Once the parameters are set click Compute to calculate a covariance matrix according to you your specifications Once the covariance matrix is ready the parts corresponding to magnetometer or axial gradiometer pla nar gradiometer and EEG channels are separated and the corresponding eigenvectors and eigenvalues are computed Once complete a projection selector with eight magnetometer eigenvectors five planar gradiometer eigenvectors thre
189. ed integer 3 4 byte signed integer 4 single precision float The epoch data are written using the big endian byte order The data are stored sample by sample First sample of this epoch in the original raw data file First sample of the epoch with respect to the event Number of samples in the epoch Table 9 7 The epochs member of the raw data info structure a Tip For source modelling purposes it is recommended that the MNE Matlab toolbox see Chapter 10 is employed to read the measurement info instead of using the channel information in the raw data info structure described in Table 9 6 MSH MNE 251 9 Data conversion 252 MSH MNE cHAPTER 10 The Matlab toolbox MSH MNE 10 1 Overview The MNE software contains a collection Matlab m files to facilitate inter facing with binary file formats of the MNE software The toolbox is located at SMNE_ROOT share matlab The names of the MNE Mat lab toolbox functions begin either with mne_ or with fiff_ When you source the mne_setup script as described in Section 2 4 on of the follow ing actions takes place 1 If you do not have the Matlab startup m file it will be created and lines allowing access to the MNE Matlab toolbox are added 2 If you have startup m and it does not have the standard MNE Matlab toolbox setup lines you will be instructed to add them manually 3 If you have startup m and the standard MNE Matlab toolbox setup lines are there nothing happens
190. ed output Required options Table 9 1 Guide to combining mne_convert_mne_data options 9 12 3 Matlab data structures The Matlab output provided by mne_convert_mne_data is organized in structures listed in Table 9 2 The fields occurring in these structures are listed in Table 9 3 The symbols employed in variable size descriptions are nloc Number of source locations nsource Number of sources For fixed orientation sources nsource nloc whereas nsource 3 nloc for free orientation sources nchan Number of measurement channels 240 MSH MNE Data conversion Ey ntime Number of time points in the measurement data lt tag gt _inv The inverse operator decomposition The forward solution lt tag gt _noise A standalone noise covari ance matrix Table 9 2 Matlab structures produced by mne_convert_mne_data The prefix given with the tag option 1s indicated lt tag gt see Section 9 12 1 Its default value is MNE wt Seen nsource x nchan The forward solution one source on each row For free orientation sources the fields of the three orthogonal dipoles for each location are listed consecutively names nchan string String array containing the names of the chan ch_names nels included ch_types nchan x 2 The column lists the types of the channels 1 MEG 2 EEG The second column lists the coil types see Tables 5 2 and 5 3 For EEG electrodes this value equals one ch_pos nchan x 3 The location informa
191. ed with 1h label or rh label depending on the hemisphere on which the label is specified 7 14 Overlays X Overlay management Available overlays Mone test Load w Load ste Delete Overlay type is _ MNE _ iMRI _j dSPM Other J sSLORETA Value histogram Color scale thresh 0 26 W Show scale bar Show comments of smooth steps E Opacity i fmia 0 49 fmax 0 79 fmult f siy gaat AT Ej ttl mA Contour step 1 0 Done show Apply to all Help Figure 7 25 The overlay management dialog In addition to source estimates derived from MEG and EEG data mne_analyze can be used to display other surface based data These over lay data can be imported from w and stc files containing single time slice static and dynamic data movies respectively These data files can be produced by mne_make_movie FreeSurfer software and custom pro grams or Matlab scripts MSH MNE Interactive analysis 7 MSH MNE The names of the files to be imported should end with lt hemi gt lt type gt where lt hemi gt indicates the hemisphere 1h or rh and lt type gt is w or Stc Overlays are managed from the dialog shown in Figure 7 25 which is invoked from File Manage overlays This dialog contains the following controls List of overlays loaded Lists the names of the overlays loaded so far Load w Load a static overlay from a w file In the op
192. en dialog it is possible to specify whether this file contains data for the cortical surface or for scalp Scalp overlays can be viewed in the viewer window Load stc Load a dynamic overlay from an stc file In the open dialog it is pos sible to specify whether this file contains data for the cortical sur face or for scalp Scalp overlays can be viewed in the viewer window Delete Delete the selected overlay from memory Time scale slider Will be activated if a dynamic overlay is selected Changes the cur rent time point Overlay type is Selects the type of the data in the current overlay Different default color scales are provided each overlay type Value histogram Shows the distribution of the values in the current overlay For large stc files this may take a while to compute since all time points are included The histogram is colored to reflect the current scale set tings The fthresh fmid and fmax values are indicated with vertical bars Color scale Sets the color scale of the current overlay To activate the values press Show For information on color scale settings see Table 7 1 Options Display options This a subset of the options in the MNE prefer ences dialog For details see Section 7 12 1 185 Ea Interactive analysis 186 Show Show the selected overlay and assign the settings to the current overlay Apply to all Apply the current settings to all loaded overlays It is also possible to in
193. en the surfaces is also computed 2 Text files containing the boundary surface vertex coordinates are cre ated 3 The the geometry dependent BEM solution data are computed This step can be optionally omitted This step takes several minutes to com plete This step assigns the conductivity values to the BEM compartments For the scalp and the brain compartments the default is 0 3 S m The defalt skull conductivity is 50 times smaller i e 0 006 S m Recent publica tions see Section 13 3 report a range of skull conductivity ratios ranging from 1 15 Oostendorp et al 2000 to 1 25 1 50 Slew et al 2009 Congalves et al 2003 The MNE default ratio 1 50 is based on the typi cal values reported in Congalves et al 2003 since their approach is based comparison of SEF SEP measurements in a BEM model The vari 25 a The Cookbook 26 ability across publications may depend on individual variations but more importantly on the precision of the skull compartment segmentation This processing stage is automated with the script mne_setup_forward_model This script assumes that 1 The anatomical MRI processing has been completed as described in Section 3 3 2 The BEM model meshes have been created as outlined in Section 3 6 3 The environment variable SUBJECTS_DIR is set correctly mne_setup_forward_model accepts the following options subject lt subject gt Defines the name of the subject This can be also acco
194. entries starting with FIFF_POINT Identifier for this point single 3 The location of this point Table 10 22 The dig structure ee ee ae C coildefs double num_points 7 Each row contains the integration point weight followed by location m and normal FV Struct Contains the faces and vertices which can be used to draw the coil for visualization Table 10 23 The coildef structure For more detailed information see Section 5 8 MSH MNE 267 The Matlab toolbox int32 Scanning order number starting from 1 order number Scanning order number starting from 1 from 1 logno int32 Logical channel number conventions in the usage of this number vary kind int32 The channel type FIFFV_MEG_CH FIFF_EEG_CH etc see Table 10 15 range double The hardware oriented part of the calibration factor This should be only applied to the continuous raw data The calibration factor to bring the channels to physical units loc double 12 The channel location The first three numbers indicate the location m followed by the three unit vectors of the channel specific coordinate frame These data contain the values saved in the fif file and should not be changed The values are specified in device coordinates for MEG and in head coordinates for EEG channels respectively coil_trans double 4 4 Initially transformation from the channel coordinates to device coordinates This transformation is updated by calls to fiff_tra
195. ents in the cortical pyramidal neurons Since the net primary current associated with these microscopic events is oriented nor mal to the cortical mantle it is reasonable to use the cortical normal orien tation as a constraint in source estimation In addition to allowing completely free source orientations the MNE software implements three orientation constraints based of the surface normal data 1 Source orientation can be rigidly fixed to the surface normal direction the ixed option If cortical patch statistics are available the aver age normal over each patch md are used to define the source orienta MSH MNE The current estimates Lo MSH MNE 6 2 10 6 2 11 tion Otherwise the vertex normal at the source space location is employed 2 A location independent or fixed loose orientation constraint LOC can be employed the Loose option In this approach a source coordinate system based on the local surface orientation at the source location is employed By default the three columns of the gain matrix G associated with a given source location are the fields of unit dipoles pointing to the directions of the x y and z axis of the coordinate sys tem employed in the forward calculation usually the MEG head coor dinate frame For LOC the orientation is changed so that the first two source components lie in the plane normal to the surface normal at the source location and the third component is aligned with it
196. er information The Time stamped Annotation Lists TALs on 221 9 Data conversion 222 the annotation data can be converted to a trigger channel STI 014 using an annotation map file which associates an annotation label with a number on the trigger channel The TALs can be listed with the listtal option see below Warning The data samples in a BDF file are represented in a 3 byte 24 bit format Since 3 byte raw data buffers are not presently supported in the fif format these data will be changed to 4 byte integers in the conver sion Since the maximum size of a fif file is 2 GBytes the maximum size of a BDF file to be converted is approximately 1 5 GBytes Warning The EDF EDF BDF formats support channel dependent sam pling rates This feature 1s not supported by mne_edf2fiff However the annotation channel in the EDF format can have a different sampling rate The annotation channel data is not included in the fif files output 9 2 8 2 Using mne_edf2fiff The command line options of mne_edf2fiff are version Show the program version and compilation date help List the command line options edf lt filename gt Specifies the name of the raw data file to process tal lt filename gt List the time stamped annotation list TAL data from an EDF file here This output is useful to assist in creating the annotation map file see the annotmap option below This output file is an event file compatible with mn
197. er realistic conditions however a gt 0O and there is a misfit between measured data and those predicted by the MNE Comparison of the pre dicted data here denoted by x t and measured one can give valuable insight on the correctness of the regularization applied In the SVD approach we easily find x t Gj C UWO where the diagonal matrix IT has elements 1 A The predicted data 1S thus expressed as the weighted sum of the recolored eigenfields in C U Cortical patch statistics If the cps option was used in source space creation see Section 3 5 or if mne_add_patch_info described in Section 11 7 was run manually the source space file will contain for each vertex of the cortical surface the information about the source space point closest to it as well as the dis tance from the vertex to this source space point The vertices for which a given source space point is the nearest one define the cortical patch asso ciated with with the source space point Once these data are available it is straightforward to compute the following cortical patch statistics CPS for each source location d 1 The average over the normals of at the vertices in a patch na 2 The areas of the patches A and 3 The average deviation of the vertex normals in a patch from their aver age Oy given in degrees The orientation constraints The principal sources of MEG and EEG signals are generally believed to be postsynaptic curr
198. ers instead of millimeters This option applies to text format files only This defini tion does not affect the units of the shift option id lt number gt Identification number to assign to this surface 1 inner skull 3 outer skull 4 scalp ico lt number gt Downsample the surface to the designated subdivision of an icosa hedron This option is relevant and required only if the triangula tion is isomorphic with a recursively subdivided icosahedron For MSH MNE The forward solution a MSH MNE example the surfaces produced by with mri_watershed are isomor phic with the 5th subdivision of a an icosahedron thus containing 20480 triangles However this number of triangles is too large for present computers Therefore the triangulations have to be deci mated Specifying ico 4 yields 5120 triangles per surface while ico 3 results in 1280 triangles The recommended choice is ico 4 5 6 3 Tessellation file format The format of the text format surface files is the following lt nvert gt lt vertex l gt lt vertex 2 gt lt vertex nvert gt lt ntri gt lt triangle I gt lt triangle 2 gt lt triangle ntri gt where lt nvert gt and lt ntri gt are the number of vertices and number of tri angles in the tessellation respectively The format of a vertex entry is one of the following XYZ The x y and z coordinates of the vertex location are given in mm number x y Zz A running n
199. ert_4D_cComp 0 000s mne_ctt_dig2fiff mne_kit2tiff mne _ make derivations 0 00 eee eee eee BEM mesh generation Matlab toolbox Release notes for MNE software 2 6 00000c Manual Command line options Changes to existing software 0 00 eee eee mne_add_patch_info 331 331 331 331 331 332 332 332 333 335 335 335 335 335 336 336 336 336 336 336 337 337 337 338 338 338 338 339 339 339 339 339 339 339 340 340 340 340 340 340 340 341 341 341 341 341 MNNG AAA Ze cas eevee td eoedee ae See eee Eeeees bead 341 mne_average_forward_solutions 342 mne_browse_raw and mne_process_raw 342 mne_compute_raw_inverse 0 00 cee eee eee 343 mne_convert_surface 0 0000 eee ee eee 343 mne_dump_triggers 2cc a52ceee ade baeneeneens hat 343 mne_epochs2mat 0 ee 344 mne_forward_solution 00000 ee eee eee 344 mne_list_ bem 2 000 es 344 mne_make_cor_Set 0000 ee es 344 mne_make_movie 00 00 ee es 344 mne_make_source_space 002 c eee eee 344 Mhe MGIDCSIG 6 saeco seSnwe bards brea geseaeeees oar 344 mne_project_raw 2 ee ees 344 mne_rename_channels 00 000 eee ee ees 345 mne_setup_forward_model 0000 cee aee 345 MNeE_SIMU 00 0 ee ees 345 mne_transform_pointS
200. es see Section 4 13 2 Trace color The color assigned for the averaged traces in the display can be adjusted by pressing this button MSH MNE Processing raw data 4 MSH MNE 4 6 4 6 1 4 6 2 4 6 3 4 6 4 The Process menu Average Compute covariance Compute raw data covariance Create anew SSP operator Figure 4 10 The contents of the Process menu The contents of the Process menu is shown in Figure 4 10 This menu accesses the following operations 1 Averaging according to a description file 2 Estimation of a covariance matrix according to a description file 3 Estimation of a covariance matrix from continuous raw data and 4 Estimation of the noise subspace for SSP Averaging The Average menu item pops up a file selection dialog to access a description file for batch mode averaging The structure of these files is described in Section 4 13 All parameters for the averaging are taken from the description file i e the parameters set in the averaging preferences dialog Section 4 5 9 do not effect the result Estimation of a covariance matrix The Compute covariance menu item pops up a file selection dialog to access a description file which specifies the options for the estimation of a covariance matrix The structure of these files 1s described in Section 4 14 Estimation of a covariance matrix from raw data The Compute raw data covariance menu item pops up a dialog which
201. es D MSH MNE D 2 2 D 2 3 D 2 4 previous version of the manual Note that Chapter 10 describing the Mat lab toolbox is totally new and change bars have not been used there Fur thermore Appendix B now contains all the information specific to the Martinos Center mne browse raw There are several improvements in the raw data processor mne_browse_raw mne_process_raw e Possibility to delete and add channel selections interactively has been added A nonstandard channel selection file can be now specified on the command line e Handling of CTF software gradient compensation has been added e The vertical scale of the digital trigger channel is now automatically set to accommodate the largest trigger value e It is now possible to load evoked response data sets from files Time scales of the evoked response data and data averaged in mne_browse_raw can be now set from the scales dialog Section 12 9 in Chapter 12 has been updated to employ mne_browse_raw in view ing the averages computed from the sample raw data set e Itis now possible to create new SSP operators in mne_browse_raw see Section 4 6 4 e Listing of amplitude values have been added to both the strip chart and topographical displays e Text format event files can now be loaded for easy inspection of rejected epochs for example e Handling of derived channels has been added see Sections 4 4 12 and VS e SSS information is now transferred to the covariance matri
202. esponse data from files All data sets from a file are loaded automatically and display in the average view window see Section 4 12 The data loaded are affected by the scale settings see Section 4 5 2 the filter see MSH MNE Processing raw data 4 MSH MNE 4 4 3 4 4 4 4 4 5 4 4 6 Section 4 5 1 and the options selected in the Manage averages dialog see Section 4 15 Save It is possible to save filtered and projected data into a new raw data file When you invoke the save option from the file menu you will be prompted for the output file name and a down sampling factor The sam pling frequency after down sampling must be at least three times the low pass filter corner frequency The output will be split into files which are just below 2 GB so that the fif file maximum size is not exceed If lt filename gt ends with fif or raw fif these endings are deleted After these modifications raw if is inserted after the remaining part of the file name If the file is split into multiple parts the additional parts will be called lt name gt lt number gt _raw fif For downsampling and saving options in mne_process_raw see Section 4 2 3 Change working directory Brings up a file selection dialog which allows changing of the working directory Read projection Selecting Read projection from the File menu pops up a dialog to enter a name of a file containing a signal space projection operator to be applied to
203. essing raw data 64 Ignore around stimulus ms Ignore this many milliseconds on both sides of the trigger when considering the epoch This parameter is useful for ignoring large stimulus artefacts e g from electrical somatosensory stimulation MEG grad rejection f T cm Rejection criterion for MEG planar gradiometers If the peak to peak value of any planar gradiometer epoch exceed this value it will be omitted A negative value turns off rejection for a particular channel type MEG mag rejection fT Rejection criterion for MEG magnetometers and axial gradiometers EEG rejection u V Rejection criterion for EEG channels EOG rejection u V Rejection criterion for EOG channels ECG rejection mV Rejection criterion for ECG channels MEG grad no signal fT cm Signal detection criterion for MEG planar gradiometers The peak to peak value of all planar gradiometer signals must exceed this value for the epoch to be included This criterion allows rejection of data with saturated or otherwise dysfunctional channels MEG mag no signal fT Signal detection criterion for MEG magnetometers and axial gradi ometers EEG no signal u V Signal detection criterion for EEG channels EOG no signal u V Signal detection criterion for EOG channels ECG no signal mV Signal detection criterion for ECG channels Fix trigger skew This option has the same effect as the FixSkew parameter in averag ing description fil
204. ested the entire averaged epoch is now included Guide to combining options The combination of options is quite complicated The Table 9 1 should be helpful to determine the combination of options appropriate for your needs Optional options forward model fwd lt name gt bad lt name gt out lt name gt surfsrc meg and or eeg fif forward model fwd lt name gt bad lt name gt out lt name gt surfsrc meg and or eeg forward model and fwd lt name gt bad lt name gt sensor covariance sensor covariance out lt name gt Surfsrc senscov lt name gt meg and or eeg fwd lt name gt bad lt name gt out lt name gt Senscov lt name gt noiseonly fif meg and or eeg sensor covariance mat Senscov lt name gt bad lt name gt out lt name sensor covariance eigenvalues Senscov lt name gt bad lt name gt out lt name elg Table 9 1 Guide to combining mne_convert_mne_data options MSH MNE 239 Data conversion Optional options evoked MEG EEG data mat meas lt name gt sel lt name gt out lt name set lt number gt evoked MEG EEG data meas lt name gt bad lt name gt forward model fwd lt name gt set lt number gt out lt name gt inverse operator data Inv lt name gt out lt name inverse operator data Inv lt name gt evoked MEG EEG data meas lt name gt Out lt name Desir
205. euroimaging data may have been subjected to noise cancellation employing the data from the ref erence sensor array Even though these sensor are rather far away from the brain sources mne_forward_solution takes them into account in the com putations If the data file specified with the meas option has software gradient compensation activated mne_forward_solution computes the field of at the reference sensors in addition to the main MEG sensor array and computes a compensated forward solution using the methods desci bed in Section 9 2 4 Warning If a data file specified with the meas option and that used in the actual inverse computations with mne_analyze and mne_make_movie have different software gradient compensation states the forward solu tion will be in mismatch with the data to be analyzed and the current esti mates will be slightly erroneous The EEG sphere model definition file For the computation of the electric potential distribution on the surface of the head EEG it is necessary to define the conductivities and radi uses of the spherically symmetric layers Different sphere models can be specified with the eegmodels option The EEG sphere model definition files may contain comment lines start ing with a and model definition lines in the following format lt name gt lt radiusl gt lt conductivityl gt lt radius2 gt lt conductivity2 gt When the file is loaded the layers are sorted so that the
206. ew This Chapter describes the data conversion utilities included with the MNE software 9 2 Importing data from other MEG EEG systems 9 2 1 This section describes the utilities to convert data from other MEG EEG systems into the fif format Importing 4 D Neuroimaging data The newest version of 4 D Magnes software includes the possibility to export data in fif Please consult the documentation of the Magnes system for details of this export utility However the exported fif file does not include information about the compensation channels and the weights to be applied to realize software gradient compensation To augment the Magnes fif files with the necessary information the MNE software includes the utilities mne_insert_4 D_comp mne_create_comp_data and mne_add_to_meas_info As aresult the complete 4D Magnes data conversion process involves the following steps 1 Export the raw data fif file from the Magnes system 2 If the data comes from a Magnes system where the primary helmet sensors are gradiometers instead of magnetometers run mne_fix_mag_coil_types with the magnes option to correct the channel information in the file see Section 11 4 4 3 Export a text file containing the Magnes compensation sensor data 4 Create a text file containing the appropriate compensation channel weights 5 Run mne_insert_4D_comp with the files created in the first two steps to merge compensation channel data with the original Ma
207. ewar and the head can be computed a few times per second MSH MNE Interactive analysis 7 MSH MNE The resulting location data expressed in the form of unit quaternions see http mathworld wolfram com Quaternion html and a translation The continuous HPI data can be through the File View continuous HPI data menu item which pops up a standard file selection dialog If the file specified ends with fif a fif file containing the continuous coordi nate transformation information is expected Otherwise a text log file is read Both files are produced by the Neuromag maxfilter software Once the data have been successfully loaded the dialog shown in Figure 7 29 appears It contains the following information 1 Currently selected time point and overview of the data at the current time point 2 MEG device to MEG head coordinate transformation at the current time point and the incremental transformation from the initial time point to the current file 3 Graphical display of the data 4 Controls for the graphical display The overview items are GOF Geometric mean of the goodness of fit values of the HPI coils at this time point Origin movement The distance between the head coordinate origins at the first and current time points Angular velocity Estimated current angular velocity of the head Coil movements Comparison of the sensor locations between the first and current time points The minimum maximum averag
208. face under the surf directory to be used Defaults to white mne setup source space looks for files rh lt name gt and 1h lt name gt under the surf directory overwrite An existing source space file with the same name is overwritten only if this option is specified cps Compute the cortical patch statistics This is need if current density estimates are computed see Section 6 2 8 If the patch information is available in the source space file the surface normal is considered 22 MSH MNE The Cookbook MSH MNE to be the average normal calculated over the patch instead of the normal at each source space location The calculation of this infor mation takes a considerable amount of time because of the large number of Dijkstra searches involved Sources per Source Surface area per lt number gt 2 a a spacing mm source mm Table 3 1 Recommended subdivisions of an icosahedron and an octahedron for the creation of source spaces The approximate source spacing and corresponding surface area have been calculated assuming a 1000 cm surface area per hemisphere For example to create the reconstruction geometry for Donald Duck with a 5 mm spacing between the grid points say mne setup source space subject duck donald Spacing 5 As a result the following files are created into the bem directory 1 lt subject gt lt spacing gt src fif containing the source space descrip tion in fif format 2 lt
209. false the matrix will be decal ibrated using the fields row_cals and col_cals when the compensation data are saved by the tool row_cals double Calibration factors applied to the rows of the com pensation data matrix when the data were read col_cals double Calibration factors applied to the columns of the compensation data matrix when the data were read data named matrix The compensation data matrix The row_names list the names of the channels to which this com pensation applies and the col_names the compen sation channels For more information see Section 9 2 4 Table 10 26 The comp structure The fif ID of the measurement file meas_id The ID assigned to this measurement by the acquisition S O O or during file conversion Table 10 27 The meas info structure MSH MNE 269 The Matlab toolbox highpass double Highpass corner frequency Hz Zero indicates a DC recording Lowpass corner frequency Hz ch nchan An array of channel information structures ch_names cell nchan Cell array of channel names dev_head_t trans The device to head transformation ctf_head_t trans The transformation from 4D CTFE head coordinates to Neuromag head coordinates This is only present in 4D CTF data dev_ctf_t trans The transformation from device coordinates to 4D CTF head coordinates This is only present in 4D CTF data dig dig The Polhemus digitization data in head coordinates bads cell Bad ch
210. fault but on a LINUX system some adjustments to the X server settings maybe necessary Consult your system administrator or Google for details 7 8 4 Selecting vertices When you click on the surface with the left mouse button the correspond ing vertex number and the associated value will be displayed on the mes sage line at the bottom of the display In addition the time course at this vertex will be shown see Section 7 13 1 You can also select a vertex by entering the vertex number to the text field at the bottom of the display If the MRI viewer is displayed and Track surface location in MRI is selected in the MRI viewer control dialog the cursor in the MRI slices will also follow the vertex selection see Section 7 18 The View menu choice Show coordinates brings up a window which shows the coordinates of the selected vertex on the white matter surface i e h white and rh white FreeSurfer surfaces If morphing surfaces have been loaded the coordinates of both the subject being analyzed and those of the morphing subject will be shown The Coordinates window includes the following lines MEG head Indicates the vertex location in the MEG head coordinates This entry will be present only if MEG EEKG data have been loaded Surface RAS MRI Indicates the vertex location in the Surface RAS coordinates This is the native coordinate system of the surfaces and this entry will always be present MSH MNE Interactive analysis 7
211. fied mne_forward_solution includes the deriv atives of the forward solution with respect to the dipole location coordi nates to the output file Let G E Syk om be the N han X 3 matrix containing the signals produced by three orthogo nal dipoles at location r making up Nohan X 3Nsource the gain matrix 5 The forward solution 118 G G Gy With the grad option the output from mne_forward_solution also con tains the NV aa 9N OE derivative matrix D D Dy where D Bek xk Irr Iyk Iyk Iyk 8 OB Bek Ox Oy Oz Ox Oy Oz Ox OV OZ i h where x Y and z are the location coordinates of the k dipole If the dipole orientations are to the cortical normal with the fixed option the dimensions of G and D are Nihan X N source and Nohan X 3N ource respec tively Both G and D can be read with the mne_read_forward_solution Matlab function see Table 10 1 5 10 Averaging forward solutions 5 10 1 Purpose One possibility to make a grand average over several runs of a experiment is to average the data across runs and average the forward solutions accordingly For this purpose mne_average_forward_solutions computes a weighted average of several forward solutions The program averages both MEG and EEG forward solutions Usually the EEG forward solution is identical across runs because the electrode locations do not change 5 10 2 Command line options mne_average_forward_solutions accept
212. files will be produced These additional extension files will be tagged with 001 f1if 002 fif etc evoked Produce and evoked response fif file instead of a raw data file Each trial in the CTF data file is included as a separate category condi tion The maximum number of samples in each trial is limited to 25000 MSH MNE Data conversion 9 MSH MNE infoonly Write only the measurement info to the output file do not include data During conversion the following files are consulted from the ds directory lt name gt res4 This file contains most of the header information pertaining the acquisition lt name gt hc This file contains the HPI coil locations in sensor and head coordi nates lt name gt meg4 This file contains the actual MEG data If the data are split across several files due to the 2 GByte file size restriction the extension files are called lt name gt lt number gt _meg4 lt name gt eeg This 1s an optional input file containing the EEG electrode locations More details are given below If the lt name gt eeg file produced from the Polhemus data file with CTF software is present it is assumed to contain lines with the format lt number gt lt name gt lt x cm gt lt y cm gt lt z cm gt The field lt number gt is a sequential number to be assigned to the con verted data point in the fif file lt name gt is either a name of an EEG chan nel one of left right o
213. flow of the cross subject averaging process in MNE soft ware References in parenthesis indicate sections and chapters of this manual MSH MNE 207 8 Morphing and averaging 208 8 6 2 Note The old utility mne_grand_average has been removed from the MNE software because of its inefficiency All users should adopt the com bination of mne_make_movie and mne_average_estimates instead Warning With the ico option it is now possible to generate source spaces with equal number of vertices in each subject This may lead to the wrong conclusion that stc data could be averaged without doing the mor phing step first Even with identical number vertices in the source spaces it is mandatory to process the data through mne_make_movie to create corresponding source locations before using mne_average_estimates The averager mne_average_estimates is the new utility for averaging data in stc files It requires that all stc files represent data on one individual s cortical surface and contain identical sets of vertices mne_average_estimates uses linear interpolation to resample data in time as necessary The command line arguments are version Show the program version and compilation date help List the command line options desc lt filenname gt Specifies the description file for averaging The format of this file is described below 8 6 2 1 The description file The description file for mne_average_estimates consists of a se
214. g mne setup source space ico 6 This command sets up the source space related files in directory sub jects sample bem as described in Section 3 5 MSH MNE The sample data set 12 MSH MNE 12 5 3 Boundary element models The geometry calculations for the single layer boundary element model are accomplished with the command mne setup forward model homog surf ico 4 This command sets up the homogeneous BEM model related files in directory subjects sample bem as described in section Section 3 7 In addition to the homogeneous BEM you also need the three layer BEM model which can be used for both EEG and MEG mne setup forward model surf ico 4 The above commands employ the inner skull surf outer skull surf and outer skin surf triangulation files located in subjects sample bem The option ico 4 will create a model with 5120 triangles on each surface Depending on the speed of your computer the three layer model may take quite a while to set up 12 6 Setting up a custom EEG layout A data specific EEG layout will facilitate viewing of the EEG data The MNE programs mne_browse_raw and mne_analyze look for user specific layouts in SHOME mne lout Thus you can create an EEG layout for the sample data set with the following commands mkdir p SHOME mne lout cd SSAMPLE MEG sample mne make eeg layout fif sample audvis raw fif lout SHOME mne lout sample EEG lout Please refer to Section 11 6 for more
215. g of the current distributions 11 Output of snapshots in w file format 12 Display of overlay data delivered in w and stc file formats 13 Creation of ROI label files 14 Viewing of continuous head position data delivered by Elekta Neuro mag software N Command line options Since mne_analyze is primarily an interactive analysis tool there are only a few command line options version Show the program version and compilation date 145 Ea Interactive analysis help List the command line options cd lt dir gt Change to this directory before starting subject lt name gt Specify the default subject name for surface loading digtrig lt name gt Name of the digital trigger channel The default value is STI 014 Underscores in the channel name will be replaced by spaces digtrigmask lt number gt Mask to be applied to the raw data trigger channel values before considering them This option is useful if one wants to set some bits in a don t care state For example some finger response pads keep the trigger lines high if not in use i e a finger is not in place Yet it is convenient to keep these devices permanently connected to the acquisition system The number can be given in decimal or hexadec imal format beginning with Ox or 0X For example the value 255 OXFF means that only the lowest order byte usually trigger lines 1 8 or bits O 7 will be considered Note Before starting
216. gly to be included in the output Since a standard position file is only provided for Magnes WH600 mne_insert_4D_comp only works for that type of a sys tem The fif files exported from the Magnes systems may contain slightly smaller number of samples than originally acquired because the total number of samples may not be evenly divisible with a reasonable number of samples which will be used as the fif raw data file buffer size There fore the reference channel data may contain more samples than the fif file The superfluous samples will be omitted from the end 9 2 6 Creating software gradient compensation data The utility mne_create_comp_data was written to create software gradi ent compensation weight data for 4D Magnes fif files This utility takes a text file containing the compensation data as input and writes the corre MSH MNE 217 9 Data conversion 218 9 2 7 sponding fif file as output This file can be merged into the fif file contain ing 4D Magnes data with the utility mne_add_to_meas_info The command line options of mne_create_comp_data are version Show the program version and compilation date help List the command line options In lt name gt Specifies the input text file containing the compensation data kind lt value gt The compensation type to be stored in the output file with the data This value defaults to 101 for the Magnes compensation and does not need to be changed out lt
217. gnes fif file 211 9 Data conversion 212 9 2 2 6 Run mne_create_comp_data on the file created in step 3 to make a fif file containing the compensation weights 7 Run mne_add_to_meas_info with the fif files created in steps 4 and 5 as input to result in a complete fif file containing all the necessary data Note Including the compensation channel data is recommended but not mandatory If the data are saved in the Magnes system are already com pensated there will be a small error in the forward calculations whose sig nificance has not been evaluated carefully at this time Importing CTF data The MNE software includes a utility mne_ctf2fiff based on the Brain Storm Matlab code by Richard Leahy John Mosher and Sylvain Baillet to convert data in CTF ds directory to fif format The command line options of mne_ctf2fiff are version Show the program version and compilation date help List the command line options verbose Produce a verbose listing of the conversion process to stdout ds lt directory gt Read the data from this directory omit lt filename gt Read the names of channels to be omitted from this text file Enter one channel name per line The names should match exactly with those listed in the CTF data structures By default all channels are included fif lt filename gt The name of the output file If the length of the raw data exceeds the 2 GByte fif file limit several output
218. gories If the recommended keepsamplemean option is specified in the covariance matrix definition file the baseline correction is applied to the epochs but the means at individual samples are not subtracted Thus the covariance matrix will be computed as Cn SrpjSrpj gt oF TD where R No X NP r R N ry S l Ne y gt Spf 1 8 pj sr i P l ip l where P l a p gt Srpj r p and 89 4 Processing raw data 90 R No gt NAP 1 ral which reflects the fact that V means are computed for category r It is easy to see that the expression for the covariance matrix estimate can be cast into a more convenient form cu T LY p Vous E E sam LPL PP er j Subtraction of the means at individual samples is useful if it can be expected that the evoked response from previous stimulus extends to part of baseline period of the next one 4 17 3 Combination of covariance matrix estimates Let us assume that we have computed multiple covariance matrix esti mates C1 CQ with corresponding degrees of freedom N N o We can combine these matrices together as q where a af q 2N q 4 17 4 SSP information included with covariance matrices If a signal space projection was on when a covariance matrix was calcu lated information about the projections applied is included with the cova riance matrix when it is saved These projection data are read by mne_inverse_operator and applied to
219. h allows changes to the default colors of various dis play items 57 4 Processing raw data 4 5 4 Derivations Brings up the interactive derivations editor This editor can be used to add or modify derived channels i e linear combinations of signals actually recorded Channel derivations can be also created and modified using the mne_make_derivations tool see Section 11 5 The interactive editor con tains two main areas Interactive tools for specifying a channel linear combination This tool is limited to combining up to five channels in each of the derivations Clicking Add after defining the name of the new derivation the weights of the component channels and their names adds the corresponding arithmetic expression to the text area Text area which contains the currently defined derivations as arithmetic expressions in a format identical to that used by mne_make_derivations These expressions can be manually edited before accepting the new set of derivations Initially the text area will contain the derivations already defined The Define button interprets the arithmetic expressions in the text area as new derivations and closes the dialog The Cancel button closes the dialog without any change in the derivations Recommended workflow for defining derived EEG channels and associ ated selections interactively involves the following steps 1 W 58 If desired EEG channels can be relabeled with descriptive na
220. hat you have run the appropriate setup scripts to make both MNE and FreeSurfer software available Organizing MRI data into directories Since all images comprising the multi echo FLASH data are contained in a single series it is necessary to organize the images according to the ech oes before proceeding to the BEM surface reconstruction This is accom plished by the mne_organize_dicom script which creates a directory tree with symbolic links to the original DICOM image files To run mne_organize_dicom proceed as follows 1 Copy all of your images or create symbolic links to them in a single directory The images must be in DICOM format We will refer to this directory as lt source gt 2 Create another directory to hold the output of mne_organize_dicom We will refer to this directory as lt dest gt Change the working directory to lt dest gt 4 Say mne organize dicom lt source gt Depending on the total num ber of images in lt source gt this script may take quite a while to run Progress 1s indicated by listing the number of images processed at 50 image intervals 09 MSH MNE Creating the BEM meshes A MSH MNE As a result lt dest gt will contain several directories named lt three digit number gt _ lt protocol_name gt corresponding to the different series of images acquired Spaces and parenthesis in protocol names will be replaced by underscores Under each of these directories there are one or more dire
221. he Itera tive Closest Point ICP algorithm 4 Listing of the current coordinate transformation 5 Buttons for discarding outlier points Discard and for saving and loading the coordinate transformation The saving and loading choices are Save default Saves a file which contains the MEG MRI coordinate transforma tion only The file name is generated from the name of the file from which the digitization data were loaded by replacing the ending fif with trans fif If this file already exists it will be over written without any questions asked Save MRI set This option searches for a file called COR fif in SUBJECTS_DIR SUBJECT mri T1 neuromag sets The file is copied to COR lt username gt lt date gt lt time gt fif and the current MEG MRI coordi nate transformation as well as the fiducial locations in MRI coordi nates are inserted Save Saves a file which contains the MEG MRI coordinate transforma tion only The ending trans fif is recommended The file name selection dialog as a button to overwrite Load Loads the MEG MRI coordinate transformation from the file speci fied The MEG MRI coordinate transformation files are employed in the for ward calculations The convenience script mne_do_forward solution described in Section 3 11 uses a search sequence which is compatible with the file naming conventions described above It is recommended that trans fif file saved with the Save default and Save
222. he MNE software forward calculation applies another coordinate transformation to the head coordi nate data to bring the coil locations and orientations to the MRI coordinate system If r is a row vector for the origin of the local sensor coordinate system and e e and e are the row vectors for the three orthogonal unit vec tors all given in device coordinates a location of a point ro in sensor coordinates is transformed to device coordinates rp by ry 1 fre 1 Ten where 105 5 The forward solution 106 e 0 T y 0 e 0 op 5 8 2 Calculation of the magnetic field The forward calculation in the MNE software computes the signals detected by each MEG sensor for three orthogonal dipoles at each source space location This requires specification of the conductor model the location and orientation of the dipoles and the location and orientation of each MEG sensor as well as its coil geometry The output of each SQUID sensor is a weighted sum of the magnetic fluxes threading the loops comprising the detection coil Since the flux threading a coil loop is an integral of the magnetic field component nor mal to the coil plane the output of the Ath MEG channel b can be approximated by N pad where r are a set of N integration points covering the pickup coil loops of the sensor B r kp is the magnetic field due to the current sources calculated at Frp Ngy are the coil normal directions at these poin
223. he grid of interpolation or extrapolation points can be located on the helmet or scalp surface for MEG and on the scalp surface for EEG The magnetic field and potential maps appear automatically whenever they are enabled from the viewer options see Section 7 10 2 7 11 2 Technical description Let x be an MEG or an EEG signal at channel k 1 N This signal is related to the primary current distribution J r through the lead field LAr x JE J r dG G where the integration space G in our case is a spherical surface The oblique boldface characters denote three component locations vectors and vector fields The inner product of two leadfields is defined as LIL L LAAG G 173 A Interactive analysis 174 These products constitute the Gram matrix T L Z The minimum norm estimate can be expressed as a weighted sum of the lead fields where w is a weight vector and L is a vector composed of the continuous lead field functions The weights are determined by the requirement X x LIJ Tw 1 e the estimate must predict the measured signals Hence w x However the Gram matrix is ill conditioned and regularization must be employed to yield a stable solution With help of the SVD l UAV a regularized minimum norm can now found by replacing the data match ing condition by x pw where T T co cu anda cu T respectively In the above the columns of U are th
224. he name of a text file containing the 4 x 4 matrix for the coordinate transformation from head to mri coordinates see below If the option trans is present the mri option is not required The search order for MEG MRI coordinate transformations is discussed below meas lt name gt This file is the measurement fif file or an off line average file pro duced thereof It is recommended that the average file is employed for evoked response data and the original raw data file otherwise This file provides the MEG sensor locations and orientations as well as EEG electrode locations as well as the coordinate transformation between the MEG device coordinates and MEG head based coordi nates fwd lt name gt This file will contain the forward solution as well as the coordinate transformations sensor and electrode location information and the source space data A name of the form lt name gt fwd fif is rec ommended If this option is omitted the forward solution file name is automatically created from the measurement file name and the source space name mindist lt dist mm gt Omit source space points closer than this value to the inner skull surface Any source space points outside the inner skull surface are automatically omitted The use of this option ensures that numerical inaccuracies for very superficial sources do not cause unexpected effects in the final current estimates Suitable value for this parame ter is of the orde
225. he returned struc ture indicates the initial skip in samples If you want your own routines which assume that initial skip has been removed perform indentically with the previous version subtract first_samp from the sample numbers you specify to fiff_read_raw_segment Furthermore fiff_setup_read_raw has an optional argument to allow reading of unprocessed MaxShield data acquired with the Elekta MEG systems New utilities D 3 4 1 mne_collect_transforms This utility collects coordinate transformation information from several sources into a single file see Section 9 9 D 3 4 2 mne_convert_dig_data This new utility convertes digitization Polhemus data between different file formats see Section 9 3 345 D Release notes 346 D 3 4 3 mne_edf2fiff This is a new utility to convert EEG data from EDF EDF and BDF for mats to the fif format see Section 9 2 8 D 3 4 4 mne_brain_vision2fiff This is a new utility to convert Brain Vision EEG data to the fif format see Section 9 2 10 This utility is also used by the mne_eximia_2fiff script to convert EEG data from the Nexstim eXimia EEG system to the fif format see Section 9 2 11 D 3 4 5 mne_anonymize New utility to remove subject identifying information from measurement files see Section 11 4 7 D 3 4 6 mne_opengl_test New utility for testing the OpenGL graphics performance see Section C 2 5 D 3 4 7 mne_volume_data2mri Convert data defined in a volume created with mne
226. he software to be installed 331 c Installation and configuration 332 C 2 3 C 2 4 C 2 5 cd lt dir gt Unpack the tar archive tar zxvf lt software package gt The name of the software directory under lt dir gt will be the same as the package file without the gz extension Installing from a Mac OSX disk image e Double click on the disk image file A window opens with the installer package lt name gt pkg inside e Double click the the package file The installer starts e Follow the instructions in the installer Tip The software will be installed to Applications lt name gt by default If you want another location select Choose Folder on the Select a Desti nation screen in the installer Tip To provide centralized support in an environment with Additional software MNE uses the Netpbm package http netpbm sourceforge net to cre ate image files in formats other than tif and rgb from mne_analyze and mne_browse_raw This package is usually present on LINUX systems On Mac OSX you need to install the netpbm package The recommended way to do this is to use the MacPorts Project tools see http www macports org 1 If you have not installed the MacPorts sofware goto http www macports org install php and follow the instructions to install MacPorts 2 Install the netpbm package by saying sudo port install netpbm MacPorts requires that you have the XCode developer tools and X11
227. he typical workflow needed to produce the mini mum norm estimate movies using the MNE software The workflow is summarized in Figure 3 1 MRI data raw mne_setup_analysis_csh 2 5 MEG data raw MRI data reconstructed FreeSurfer 3 3 A COR fif T1 COR fif brain mne_setup_mri 3 4 COR aligned fif T1 BEM mesh inner skull source space mne_setup_source_space 3 5 mne_analyze 7 mne_watershed A 1 Mrilab flash_bem A 2 a en MEG data filtered averaged noise covariance g l mne_browse_raw 4 BEM model mne_setup_forward_model 3 7 forward solution mne_do_forward_solution 3 11 J inverse operator mne_do_inverse_operator 3 13 4 Analyze and make movies and snapshots mne_analyze 7 mne_make_movie 6 5 4 movie files snapshots stc and w files Figure 3 1 Workflow of the MNE software References in parenthesis indicate sections and chap ters of this manual MSH MNE 19 a The Cookbook 20 3 2 Selecting the subject Before starting the data analysis setup the environment variable SUBJECTS_DIR to select the directory under which the anatomical MRI data are stored Optionally set SUBJECT as the name of the subject s MRI data directory under SUBJECTS_DIR With this setting you can avoid entering the subject option common to many MNE programs and scripts In the following sections files in the FreeSurfer directory hierar chy
228. help of the patch selection dialog which appears when File Load surface patch or File Load morphing surface patch is selected This dialog shown in Figure 7 12 contains a list of available patches and the possibility to rotate the a flat patch coun terclockwise by the specified number of degrees from its original orienta tion The patch is automatically associated with the correct hemisphere on the basis of the two first letters in the patch name lh left hemisphere rh right hemisphere O X Load a patch Available patches lh occip patch 3d lh accip patch flat selection lh occip patch flal Rotation angle deg i OK Cancel Help Figure 7 12 The patch selection dialog 7 8 3 Controlling the surface display The main surface display has a section called Adjust view which has the controls shown in Figure 7 13 Land R Select the left or right hemisphere surface loaded through File Load surface 160 MSH MNE Interactive analysis ZA MSH MNE B Display the surfaces for both hemispheres M Display the surfaces loaded File Load morphing surface accord ing to the L R and B hemisphere selectors P Select the patch associated with the currently selected surface For this to work either L or R must be selected Option menu Select one of the predefined view orientations see Section 7 8 5 below Arrow buttons Rotate the surface by increments specified in degrees in the text box
229. hemisphere If the name refers to a flat patch the name can be optionally followed by a colon and a rotation angle in degrees The flat patch will be then rotated counterclockwise by this amount before display You can check a suitable value for the rota tion angle by loading the patch interactively in mne_analyze width lt value gt Width of the graphics output frames in pixels The default width is 600 pixels height lt value gt Height of the graphics output frames in pixels The default height 1s 400 pixels mag lt factor gt Magnify the the visualized scene by this factor lh Select the left hemisphere for graphics output By default both hemisphere are processed rh Select the right hemisphere for graphics output By default both hemisphere are processed view lt name gt Select the name of the view for mov rgb and tif graphics output files The default viewnames defined in SMNE ROOT share MSH MNE The current estimates Lo MSH MNE mne mne analyze eyes are lat lateral med medial ven ventral and occ occipital You can override these defaults by cre ating the directory mne under your home directory and copying the eyes file there Each line of the eyes file contais the name of the view the viewpoint for the left hemisphere the viewpoint for the right hemisphere left hemisphere up vector and right hemisphere up vector The entities are separated by semicolons Lines beginning with
230. hen the mri option is present Even with the all option only those vertices actually selected will be marked to be in use in the output source space file 5 6 Creating the BEM meshes 5 6 1 The mne_surf2bem utility converts surface triangle meshes from ASCII and FreeSurfer binary file formats to the fif format The resulting fiff file also contains conductivity information so that it can be employed in the BEM calculations Note The utility mne_tri2fiff previously used for this task has been replaced by mne_surf2bem Tip The convenience script mne_setup_forward_model described in Section 3 7 calls mne_surf2bem with the appropriate options Note The vertices of all surfaces should be given in the MRI coordinate system Command line options This program has the following command line options version Show the program version and compilation date help List the command line options Surf lt name gt Specifies a FreeSurfer binary format surface file Before specifying the next surface surf or tri options details of the surface specification can be given with the options listed in Section 5 6 2 tri lt name gt Specifies a text format surface file Before specifying the next sur face surf or tri options details of the surface specification can be given with the options listed in Section 5 6 2 The format of these files is described in Section 5 6 3 101 Ee The forward solution 5 6 2
231. here is at least one such point over the right cheek To dis card this point 1 Click on Discard in the Adjust coordinate alignment window 2 Enter 10 for the distance of the points to be discarded 3 Click done The outlier point disappears The coordinate transformation can be adjusted manually with the arrow buttons in the middle part of the Adjust coordinate alignment dialog These buttons move the digitizer points in the directions indicated by the amount listed next to each of the buttons An automatic iterative procedure Iterative Closest Point ICP matching is also provided At each iteration step 1 For each digitizer point transformed from MEG to the MRI coordinate frame the closest point on the triangulated surface is determined 2 The best coordinate transformation aligning the digitizer points with the closest points on the head surface is computed 309 12 The sample data set 310 12 11 3 12 12 In step 2 of the iteration the nasion is assigned five times the weight of the other points since it can be assumed that the nasion is the easiest point to identify reliably from the surface image The ICP alignment can be invoked by entering the desired number of iter ations next to the CP align button followed by return or simply pressing the CP align button The iteration will converge in 10 to 20 steps Warning Use the ICP alignment option in mne_analyze with caution The iteration will not converge to a
232. hese programs please consult Chapter 4 6 For evoked response analysis the data has to be re averaged off line see Section 3 9 5 Cleaning the digital trigger channel The calibration factor of the digital trigger channel used to be set to a value much smaller than one by the Neuromag data acquisition software Especially to facilitate viewing of raw data in graph it is advisable to change the calibration factor to one Furthermore the eighth bit of the trigger word is coded incorrectly in the original raw files Both problems can be corrected by saying mne fix stiml4 lt raw file gt More information about mne_fix_stim 4 is available in Section 11 4 2 It is recommended that this fix is included as the first raw data processing step Note however the mne_browse_raw and mne_process_raw always sets the calibration factor to one internally Note If your data file was acquired on or after November 10 2005 on the Martinos center Vectorview system it is not necessary to use mne_fix_stim1l4 29 al The Cookbook 30 3 9 2 3 9 3 Fixing channel information There are two potential discrepancies in the channel information which need to be fixed before proceeding 1 EEG electrode locations may be incorrect if more than 60 EEG chan nels are acquired 2 The magnetometer coil identifiers are not always correct These potential problems can be fixed with the utilities mne_check_eeg_locations and mne_fix_mag_coil_types
233. his is a fif file containing the predicted data waveforms see Section 6 2 7 outputnorm lt name gt Output noise normalization factors to this file iInvnorm Output inverse noise normalization factors to the file defined by the outputnorm option dip lt name gt Specifies a dipole distribution snapshot file This is a file containing the current distribution at a time specified with the diptime option The file format is the ASCII dip file format produced by the Neuromag source modelling software xfit Therefore the file can be loaded to the Neuromag MRIlab MRI viewer to display the actual current distribution This option is only effective if the Spm option is absent diptime lt time ms gt Time for the dipole snapshot see dip option above label lt name gt Label to process The label files are produced by tksurfer and spec ify regions of interests ROIs A label file name should end with lh label for left hemisphere ROIs and with rh label for right hemisphere ones The corresponding output files are tagged 329 B Setup at the Martinos Center with 1h lt data type amp and rh lt data type amp respec tively lt data type gt equals MNE for expected current data and spm for dSPM data Each line of the output file contains the waveform of the output quantity at one of the source locations falling inside the ROI Note The tmin and tmax options which existed in previous ver sions of
234. his section describes how the covariance matrices are computed for raw data and epochs Continuous raw data If a covariance matrix of a raw data is computed the data are checked for artefacts in 200 sample pieces Let us collect the accepted M samples from all channels to the vectors Sj j 1 M The estimate of the covariance matrix is then computed as M A E 1 z T C TDA S S S S j l where is the average of the signals over all times Note that no attempt is made to correct for low frequency drifts in the data If the contribution of any fre quency band is not desired in the covariance matrix estimate suitable band pass filter should be applied For actual computations it is convenient to rewrite the expression for the covariance matrix as M l T M wt C S S SS i2 JJ M l j l MSH MNE Processing raw data 4 MSH MNE 4 17 2 Epochs The calculation of the covariance matrix is slightly more complicated in the epoch mode If the bmin and bmax parameters are specified in the covariance matrix description file see Section 4 14 3 baseline correction is first applied to each epoch Let the vectors S pj P Pj l eo Npr l R be the samples from all channels in the baseline corrected epochs used to calculate the covariance matrix In the above P is the number of accepted epochs in category r N is the number of samples in the epochs of category r and R is the number of cate
235. i94245ucanneeueus dgbabeteeeehueyders 70 4 10 Events and annotations 02 00 c eee es 71 OVGIVIEW 66 44 be euaea ae Be onte ks ba barddas deka na nae ea 71 The event list 0 0 00 ees 71 Loading and saving event files nananana aaea 72 Defining annotated events 2 000 eee ee eee 73 E E E 13 4 11 The tool bar s4ceuwectse ceetereaes Cog ee eee eed ee ees 74 4 12 Topographical data displays 0200 eee eee 76 4 13 Description files for off line averaging 0005 76 Overall format 0 0 0 eee 7 Common parameters 0 000 ccc ee ees 77 Category definition nannaa aa aaa nee 79 4 14 Description files for covariance matrix estimation 80 Overall format oso ues ured naaa oe ee hare 81 Common parameters 0 0 00 ccc ee ee eee 81 Covariance definitions 0 00 0 ce eee 83 4 15 Managing averages 0 0 c eee ee ees 84 MSH MNE 4 16 The Signal Space Projection SSP method 85 General concepts 0 00 ee ees 85 Estimation of the noise Subspace 000 eee 87 EEG average electrode reference 00000 ee 87 4 17 Covariance matrix estimation 0000008 88 Continuous raw data 0 0 cc ee ee 88 EDOCHS 4 ob akecde rE oS es eee tara ep hoeueeese ewe eases 89 Combination of covariance matrix estimates 90 SSP information included with covariance matrices 90 4 18
236. iance matrix is output Srccov lt name gt Specifies the fif file containing the source covariance matrix to be included with the output Only diagonal source covariance files can be handled at the moment bad lt name gt Specifies the name of the file containing the names of the channels to be omitted one channel name per line This does not affect the output of the inverse operator since the channels have been already selected when the file was created 23 9 Data conversion 238 fif mat Output the forward model and the noise covariance matrix into measurement fif files The forward model files are tagged with lt modalities gt meas fwd fif and the noise covariance matrix files with lt modalities gt meas cov f if Here modalities is meg if MEG is included eeg if EEG is included and meg eeg if both types of signals are present The inclusion of modalities 1s controlled by the meg and eeg options Output the data into MATLAB mat files This 1s the default The for ward model files are tagged with lt modalities gt fwd mat forward model and noise covariance matrix output with inv mat for inverse operator output and with inv meas mat for combined inverse operator and measurement data output respectively The meaning of lt modalities gt is the same as in the fif output described above tag lt name gt By default all variables in the matlab output files start with MNE_ This option
237. icients will be set to unity elp lt filename gt The name of the electrode location file If this file is missing the electrode locations will be unspecified This file is in the probe file format used by the Source Signal Imaging Inc software For description of the format see http www sourcesignal com formats_probe html The fiducial marker locations optional in the probe file format specification are mandatory for mne_tufts2 fiff Note that some other software packages may produce electrode position files with the e p ending not conforming to the above speci fication MSH MNE Data conversion 9 MSH MNE 9 2 10 Note The conversion process includes a transformation from the Tufts head coordinate system convention to that used in the Neuromag systems Important The fiducial landmark locations optional in the probe file format must be present for mne_tufts2fiff Importing BrainVision EEG data The utility mne_brain_vision2fiff was created to import Brain Vision EEG data This utility also helps to import the eXimia Nexstim TMS compat ible EEG system data to the MNE software The utility uses an optional fif file containing the head digitization data to allow source modeling The MNE Matlab toolbox contains the function fiff_write_dig_file to write a digitization file based on digitization data available in another format see Chapter 10 The command line options of mne_brain_vision2fiff are yer
238. ied with the fmri option If the value is in the a priori files falls below this value at a particular source space point the source covariance matrix values are multiplied by the value specified with the fmrioff option default 0 1 Other wise it 1s left unchanged fmrioff lt value gt The value by which the source covariance elements are multiplied if the a priori weight falls below the threshold set with fmrithresh see above bad lt name gt A text file to designate bad channels listed one channel name on each line of the file If the noise covariance matrix specified with the Ssenscov option contains projections bad channel lists can be included only if they specify all channels containing non zero entries in a projection vector For example bad channels can usually specify all magnetometers or all gradiometers since the projection vectors for these channel types are completely separate Similarly it is possible to include MEG data only or EEG data only by using 131 6 The current estimates 132 6 5 only one of meg or eeg options since the projection vectors for MEG and EEG are always separate Surfsrc Use a source coordinate system based on the local surface orienta tion at the source location By default the three dipole components are pointing to the directions of the x y and z axis of the coordinate system employed in the forward calculation usually the MEG head coordinate frame This opti
239. ifies the starting time employed in the analysis If tmin option is missing the analysis starts from the beginning of the epoch tmax lt time ms gt Specifies the finishing time employed in the analysis If tmax option is missing the analysis extends to the end of the epoch tstep lt step ms gt Time step between consequtive movie frames specified in millisec onds 133 6 The current estimates 134 integ lt At ms gt Integration time for each frame Defaults to zero The integration will be performed on sensor data If the time specified for a fram 1s fo the integration range will be t At 2 lt t lt t At 2 pick lt time ms gt Pick a time for the production of rgb tif jpg png or w files Several pick options may be present The time must be with in the analysis interval indicated by the tmin and tmax options The rgb tif jpg png and w options control which file types are actually produced When a pick option is encountered the effect of any preceeding pickrange option is ignored pickrange All previous pick options will be ignored Instead snapshots are produced as indicated by the tmin tmax and tstep options This is useful e g for producing input for scripts merging the individual graphics snapshots into a composite filmstrip rep rensentation However such scripts are not yet part of the MNE software bmin lt time ms gt Specifies the
240. ift the scalp surface outwards along the vertex normal directions by this amount nosol Omit the BEM model geometry dependent data preparation step This can be done later by running mne_setup_forward_model with out the nosol option model lt name gt Name for the BEM model geometry file The model will be created into the directory bem as lt name gt bem fif If this option is miss ing standard model names will be used see below As a result of running the mne_setup_foward_model script the following files are created into the bem directory 1 BEM model geometry specifications lt subject gt lt ntri scalp gt lt ntri outer_Skull gt lt ntri inner_skull gt bem 1 or lt subject gt lt ntri inner_skull gt bem 1if containing the BEM geometry in fif format 2 al The Cookbook 28 The latter file is created if homog option is specified Here lt ntri xxx gt indicates the number of triangles on the corresponding surface 2 lt subject gt lt surface name gt lt ntri gt pnt files are created for each of the surfaces present in the BEM model These can be loaded to MRIlab to check the location of the surfaces 3 lt subject gt lt surface name gt lt ntri gt surf files are created for each of the surfaces present in the BEM model These can be loaded to tkmedit to check the location of the surfaces 4 The BEM solution file containing the geometry dependent solution data will be produced
241. ile identical The value at each source location is the maximum value of the output quantity at this location over the analysis period This option is convenient for determining the correct thresholds for the rendering of the final brain activity movies collapsel Make all frames in the stc file or the wfile indentical The value at each source location is the L norm of the output quantity at this location over the analysis period MSH MNE Setup at the Martinos Center B MSH MNE collapse2 Make all frames in the stc file or the wfile identical The value at each source location is the L norm of the output quantity at this location over the analysis period SIcurrents Output true current values in SI units A m By default the currents are scaled so that the maximum current value is set to 50 Am out lt name gt Specifies the output file name This is the stem of the output file name The actual name is derived by removing anything up to and including the last period from the end of lt name gt According to the hemisphere 1h or rh is then appended Finally stc or w is added depending on the output file type wfiles Use binary w files in the output whenever possible The noise nor malization factors can be always output in this format The current estimates and dSPMs can be output as wfiles if one of the collapse options is selected pred lt name gt Save the predicted data into this file T
242. ile 1s described in Section 9 3 1 fif lt name gt Specifies the output fif file MSH MNE Data conversion 9 MSH MNE 9 2 4 Applying software gradient compensation Since the software gradient compensation employed in CTF systems is a reversible operation it is possible to change the compensation status of CTF data in the data files as desired This section contains information about the technical details of the compensation procedure and a descrip tion of mne_compensate_data which is a utility to change the software gradient compensation state in evoked response data files The fif files containing CTF data converted using the utility mne_ctf2fiff contain several compensation matrices which are employed to suppress external disturbances with help of the reference channel data The refer ence sensors are located further away from the brain than the helmet sen sors and are thus measuring mainly the external disturbances rather than magnetic fields originating in the brain Most often a compensation matrix corresponding to a scheme nicknamed Third order gradient com pensation is employed Let us assume that the data contain n MEG sensor channels n refer ence sensor channels and n other channels The data from all channels can be concatenated into a single vector j x T T T a where x X and x are the data vectors corresponding to the MEG sen sor channels reference sensor channels and other channels re
243. iles and interprets the sample numbers appro priately However the recognition of the old and new event file formats depends on the initial pseudo event and therefore this first event should never be removed from the new event files Likewise if an initial pseudo event with lt from gt and lt to gt fields equal to zero is added to and old event file the results will be unpredictable Note If you have created Matlab Excel or other scripts to process the event files they may need revision to include the initial pseudo event in order for mne_browse_raw and mne_process_raw to recognize the edited event files correctly Note Events can be also stored in fif format This format can be read and written with the Matlab toolbox functions mne_read_events and mne_write_events 4 11 The tool bar start s oono Remove dc Keep dc Jump to In gt Picked to 000 Forget i000 Average fi sample_audvis_raw fif Vertex T 0 0000 2002 12 03 14 01 53 676 9 9998 s Figure 4 14 The tool bar controls MSH MNE Processing raw data 4 MSH MNE The tool bar controls are shown in Figure 4 14 They perform the follow ing functions Start s Allows specification of the starting time of the display as a numeric value Note that this value will be rounded to the time of the nearest sample when you press return If you click on this text field you can also change the time with the up and down cursor keys 1 10 of the wind
244. ilities 11 MSH MNE yersion Show the program version and compilation date help List the command line options fif lt name gt Specifies the name of the data file to modify alias lt name gt Specifies the text file which contains the modifications to be applied see below revert Reverse the roles of old and new channel names in the alias file Each line in the alias file contains the old name and new name for a chan nel separated by a colon The old name is a name of one of the channels presently in the file and the new name is the name to be assigned to it The old name must match an existing channel name in the file exactly The new name may be followed by another colon and a number which is the channel type to be assigned to this channel The channel type options are listed in Table 11 1 Channel Corresponding co i Table 11 1 Channel types Warning Do not attempt to designate MEG channels to EEG channels or vice versa This may result in strange errors during source estimation Tip You might consider renaming the EEG channels with descriptive labels related to the standard 10 20 system This allows you to use stan dard EEG channel names when defining derivations see Sections 11 5 279 1 Miscellaneous utilities 280 11 4 6 and 4 4 12 as well as in the channel selection files used in mne_browse_raw see Section 4 5 5 Modifying trigger channel data mne_add_triggers 11 4 6 1 Purpose
245. imates directly The batch mode version of mne_brawse_raw is called mne_process_raw Detailed information on mne_browse_raw and mne_process_raw can be found in Chapter 4 3 10 Aligning the coordinate frames The calculation of the forward solution requires knowledge of the relative location and orientation of the MEG EEG and MRI coordinate systems The MEG EEG head coordinate system is defined in Section 5 3 The conversion tools included in the MNE software take care of the idiosyn crasies of the coordinate frame definitions in different MEG and EEG sys tems so that the fif files always employ the same definition of the head coordinate system Ideally the head coordinate frame has a fixed orientation and origin with respect to the head anatomy Therefore a single MRI head coordinate transformation for each subject should be sufficient However as explained in Section 5 3 the head coordinate frame is defined by identify ing the fiducial landmark locations making the origin and orientation of the head coordinate system slightly user dependent As a result the most conservative choice for the definition of the coordinate transformation computation is to re establish it for each experimental session i e each time when new head digitization data are employed The interactive source analysis software mne_analyze provides tools for coordinate frame alignment see Chapter 7 Section 12 11 also contains tips for using mne_analyze for this pu
246. in Chapter 3 Important Going through the analysis exercise in this chapter is not a substitute for reading other chapters of this manual and understanding the concepts underlying MNE software 12 2 Overview The MNE software is accompanied by a sample data set which includes the MRI reconstructions created with FreeSurfer and the an MEG EEG data set These data were acquired with the Neuromag Vectorview system at MGH HMS MIT Athinoula A Martinos Center Biomedical Imaging EEG data from a 60 channel electrode cap was acquired simultaneously with the MEG The original MRI data set was acquired with a Siemens 1 5 T Sonata scanner using an MPRAGE sequence Important These data are provided solely for the purpose of getting familiar with the MNE software They should not be redistributed to third parties The data should not be used to evaluate the performance of the MEG or MRI system employed In the MEG EEG experiment checkerboard patterns were presented into the left and right visual field interspersed by tones to the left or right ear The interval between the stimuli was 750 ms Occasionally an smiley face was presented at the center of the visual field The subject was asked to press a key with the right index finger as soon as possible after the appear 299 12 The sample data set 300 12 3 ance of the face A listing of the corresponding trigger codes is provided in Table 12 1 nme a OO s Response to left ear auditory sti
247. in files FIFFV_MNE_ FIFFV_MNE_COORD_TUFTS_EEG _TUFTS_EEG FIFFV_MNE_COORD_TUFTS_EEG 300 The Tufts EEG data coordinate frame The Tufts EEG data coordinate frame Tufts EEG data coordinate frame FIFFV_MNE_COORD_CTF_DEVICE 1001 The CTF device coordinate frame does not appear in files FIFFV MNE COORD CTF HEAD 1004 The CTF 4D head coordinate frame FIFFV_ ASPECT STD ERR Data aspect standard error of mean FIFFV_ASPECT_SINGLE Single epoch FIFFV FIFFV_ASPECT_SUBAVERAGE SUBAVERAGE One subaverage FIFFV Care PECT_ALTAVERAGE FIFFV_ASPECT_SAMPLE A sample cut from raw data FIFFV_ASPECT_POWER_DENSITY Power density spectrum FIFFV_ASPECT_DIPOLE_WAVE The time course of an equivalent cur rent dipole One plus minus subaver FIFFV_POINT_CARDINAL Digitization point which is a cardinal landmark aka fiducial point FIFFV_ FIFFV_POINT_HPI HPI Digitized HPI coil location Table 10 15 FIFF constants MSH MNE 263 10 The Matlab toolbox ame vue nesepi FIFFV MNE_ FIXED ORI l Fixed orientation constraint used in the computation of a forward solution FIFFV MNE FREE ORI 2 No orientation constraint used in the computation of a forward solution FIFFV_MNE_ MEG Indicates an inverse operator based on MEG only FIFFV_MNE_ EEG Indicates an inverse operator based on EEG only FIFFV MNE MEG EEG Indicates an inverse operator based on both MEG and EEG FIFFV_MNE_SENSOR_COV Synonym for FIFFV_MNE_NOISE_COV l FIFFV MNE FMRI
248. information on mne_make_eeg_layout Note It is usually sufficient to create one EEG layout for each electrode cap you are using in your experiment rather than using a different layout file for each data file generated using the same cap 12 7 Previewing the data Previewing your raw data before proceeding to averaging and computa tion of the current estimates is most important to avoid unintentional errors caused by noisy or dysfunctional channels frequent eye blinks inappropriate bandpass filtering etc 303 12 The sample data set One possible routemap for the preview session is outlined below 304 1 Launch mne_browse_raw Open the raw data file sample audvis raw fif from File OO Go to the MEG EEG data directory cd SAMPLE MEG sample Open Switch all SSP vectors off from Adjust Projection Set the lowpass filter corner to a high value e g 150 Hz from Adjust Filter Browse through all channels using the selections available under Adjust Selection and look for very noisy or flat channels You should be able to readily identify two such channels among all MEG and EEG channels You may need to click Remove DC to reliably associate the noisy or flat waveform with the channel name on the left Also experi ment with switching the EEG average reference projection on and off and you will notice that the EEG bad channel cannot be seen after the projection Mark the channels you identified
249. ing history block or the lt to gt file already has it the destination file remains unchanged 11 5 Creating a derivation file 11 5 1 Purpose In mne_browse_raw channel derivations are defined as linear combina tions of real channels existing in the data files The utility mne_make_derivations reads derivation data from a suitably formatted text file and produces a fif file containing the weights of derived channels as a Sparse matrix Two input file formats are accepted 1 A file containing arithmetic expressions defining the derivations and 2 A file containing a matrix which specifies the weights of the channels in each derivation Both of these formats are described in MSH MNE Miscellaneous utilities 11 11 5 2 11 5 3 MSH MNE Command line options mne_make_derivations recognizes the following command line options version Show the program version and compilation date help List the command line options In lt name gt Specifies a measurement file which contains the EEG electrode locations This file is not modified Inmat lt name gt Specifies the output file where the layout is stored Suffix lout is recommended for layout files mne_analyze and mne_browse_raw look for the custom layout files from the directory SHOME mne lout trans Indicates that the file specified with the inmat option contains a transpose of the derivation matrix thresh lt value gt Specifies the threshold
250. interval between the frames as well as the quality of the movies which is restricted to the range 25 100 The size of the QuickTime file produced is approximately proportional to the quality Available file types JPEG Jpg TIFF ti RGB rgb PDF paf i JPNG png Output mode single A Selection Jsers mshdata sample dataMEGsample Figure 7 16 File type selection in the image saving dialog MSH MNE 165 A Interactive analysis 166 UII GOUT SE MICA yu LE SUTAL ulti course ME Gigb test pc F p fe ad p Time range for the movie starting time ms IP 103 2 Finishing time ms i ss Time step ms E jo JPEG quality 0 100 selection Jsersimsh data mult_ course MEG gb test OK Fitter Cancel Help Ooo 2 Figure 7 17 The controls in the movie saving dialog 7 8 8 Image output modes The image saving dialog shown in Figure 7 16 selects the format of the image files produced and the image output mode The buttons associated with different image format change the file name filter in the dialog to dis play files of desired type However the final output format is defined by the ending of the file name in the Selection text field as follows Jpg JPEG Joint Photographic Experts Group format Best quality jpeg is always produced tif or tiff Uncompressed TIFF Tagged Image File Format rgb RGB format pdf Portable Docu
251. ion magFlat lt value T gt Signal detection criterion for MEG magnetometers and axial gradi ometers channels eegF lat lt value V gt Signal detection criterion for EEG channels eogFlat lt value V gt Signal detection criterion for EOG channels MSH MNE Processing raw data 4 ecgFlat lt value V gt Signal detection criterion for ECG channels stimIgnore lt time s gt Ignore this many seconds on both sides of the trigger when consid ering the epoch This parameter is useful for ignoring large stimulus artefacts e g from electrical somatosensory stimulation fixSkew Since the sampling of data and the stimulation devices are usually not synchronized all trigger input bits may not turn on at the same sample If this option is included in the off line averaging descrip tion file the following procedure is used to counteract this if there is a transition from zero to a nonzero value on the digital trigger channel at sample n the following sample will be checked for a transition from this nonzero value to another nonzero value If such an event pair is found the two events will be jointly considered as a transition from zero to the second non zero value keepsamplemean The means at individual samples will not be subtracted in the esti mation of the covariance matrix For details see Section 4 17 2 This parameter is effective only for estimating the covariance matrix from epochs It is recommended to sp
252. ion date help List the command line options lspcov lt name gt The LISP noise covariance matrix file to be converted meas lt name gt A fif format measurement file used to assign channel names to the noise covariance matrix elements This file should have precisely the same channel order within MEG and EEG as the LISP format covariance matrix file out lt name gt The name of a fif format output file The file name should end with cov fif text format output file No information about the channel names is included The covariance matrix file is listed row by row This file can be loaded to MATLAB for example outasc lt name gt The name of a text format output file No information about the channel names is included The covariance matrix file is listed row by row This file can be loaded to MATLAB for example 9 12 The MNE data file conversion tool This utility called mne_convert_mne_data allows the conversion of vari ous fif files related to the MNE computations to other formats The two principal purposes of this utility are to facilitate development of new anal ysis approaches with Matlab and conversion of the forward model and noise covariance matrix data into evoked response type fif files which can be accessed and displayed with the Neuromag source modelling software Important Most of the functions of mne_convert_mne_data are now covered by the MNE Matlab toolbox covered in Chapter 10 This toolbox
253. ion in mne_analyze is not transferred to mne_browse_raw Scales The vertical scales are kept synchronized between the two pro grams In addition the settings of the sample time limits are com municated from mne_browse_raw to mne_analyze Filter The filter settings are kept synchronized 91 4 Processing raw data 92 MSH MNE cuapters the forward solution 5 1 Overview This Chapter covers the definitions of different coordinate systems employed in MNE software and FreeSurfer the details of the computation of the forward solutions and the associated low level utilities 5 2 MEG EEG and MRI coordinate systems The coordinate systems used in MNE software and FreeSurfer and their relationships are depicted in Figure 5 1 Except for the Sensor coordi nates all of the coordinate systems are Cartesian and have the RAS Right Anterior Superior orientation i e the x axis points to the right the y axis to the front and the z axis up MEG EEG MRI T Head coordinates Surface RAS MRI coordinates LE T T MRI Talairach coordinates Teele FreeSurfer Talairach coordinates z lt 0 Sensor coordinates FreeSurfer Talairach coordinates z gt 0 Figure 5 1 MEG EEG and MRI coordinate systems The coordinate transforms present in the fif files in MNE and the FreeSurfer files as well as those set to fixed values are indicated with T where x identifies the transformation M
254. ions 242 es c2 6iigh42284se0ee0 644 5 7 16 Coordinate frame alignment 200000e eee Using a high resolution head surface tessellation Using fiducial points identified by other software 7 17 Viewing continuous HPI data 0000 eee eee 7 18 Working with the MRI viewer 0000 eens 7 19 Working with the average brain 00000eaeee 7 20 Compatibility with cliplab 00000 ee Chapter 8 Morphing and averaging 8 1 OVEWICW stokncvewececeeeaseviasnsiaeencisebered es 8 2 The morphing Maps 02 00 c eee ee 8 3 About smoothing 00sec eee ee 8 4 Precomputing the morphing maps 0 55 8 5 Morphing label data 0 00 c eee es 8 6 Averaging c4 0cecneeeeneew ba ct eeee eee en eweh eee OVEIVIEW 1 0 ee eee eens The averager 0 ccc ee eens The description file 0 0 00 cece Chapter 9 Data conversion MSH MNE 9 1 OVGIWIGW fee enka cae et esse ees aes set eene cee eee 9 2 Importing data from other MEG EEG systems Importing 4 D Neuroimaging data 000 eee Importing CTF data 4 0nae55 426s 2 beedaweeeu do4 oe ee o Importing CTF Polhemus data 00 0000 eee Applying software gradient compensation 203 203 203 204 205 206 207 207 208 208 211 211 211 211 212 214 215 9 14 Chapter 10 10 1 10 2 10 3 Chapter 11 vi 11 1 11 2 11
255. is coordinate system is at the center of the con formed FreeSurfer MRI volumes usually 256 x 256 x 256 isotropic l mm voxels and the axes are oriented along the axes of this vol ume The BEM surface and the locations of the sources in the source space are usually expressed in this coordinate system in the fif files In this manual the Surface RAS coordinates are usually referred to as MRI coordinates unless there is need to specifically discuss the different MRI related coordinate systems RAS coordinates This coordinate system has axes identical to the Surface RAS coor dinates but the location of the origin is different and defined by the original MRI data i e the origin is in a scanner dependent location There is hardly any need to refer to this coordinate system explicitly in the analysis with the MNE software However since the Talairach coordinates discussed below are defined with respect to RAS coor dinates rather than the Surface RAS coordinates the RAS coordi nate system is implicitly involved in the transformation between Surface RAS coordinates and the two Talairach coordinate systems MSH MNE The forward solution a MSH MNE MNI Talairach coordinates The definition of this coordinate system is discussed e g in http imaging mrc cbu cam ac uk imaging MniTalairach This transfor mation is determined during the FreeSurfer reconstruction process FreeSurfer Talairach coordinates The problem with the MNI Ta
256. is realized in the frequency domain and has a zero phase shift When a filter is in effect the value of the first sample in the file is sub tracted from the data to correct for an initial dc offset This procedure also eliminates any filter artifacts in the beginning of the data Note The filter affects both the raw data and evoked response data loaded from files However the averages computed in mne_browse_raw and shown in the topographical display are not refiltered if the filter is changed after the average was computed 4 5 2 Scales Selecting Scales from the Adjust menu pops up the dialog shown in Figure 4 6 Adjust scales settings for raw data segments and averages MEG fT em 400 0 Time span 3 ioo Scale magnification for averages an MEG axmult cm B00 _ Show stimulus markers Average display baseline min ms E1000 EEG uv Vann soos a Cina ile 2 oso Average display baseline max ms 0 0 EOG fu asoa segment max time 3 a o W Use average display baseline ECG mv i show segments in full view Average time range min ms igg Show segments in sample view A ti EMG mv i Verage time range max ms fhe Show channel names WA utoscale time range Be i Text size 010 J Show viewport frames J Show zeroline and zerolevel OK Apply Cancel Help Figure 4 6 The Scales dialog MSH MNE 55 4 Processing raw data 56 The items in the dialog have the following functions M
257. is recommended to avoid creating additional files occupying disk space MSH MNE Data conversion 9 MSH MNE 9 12 1 Command line options The command line options recognize by mne_convert_mne_data are yersion Show the program version and compilation date help List the command line options fwd lt name gt Specity the name of the forward solution file to be converted Chan nels specified with the bad option will be excluded from the file fixed Convert the forward solution to the fixed orientation mode before outputting the converted file With this option only the field patterns corresponding to a dipole aligned with the estimated cortex surface normal are output Surfsrc When outputting a free orientation forward model three orthogonal dipole components present rotate the dipole coordinate system at each source node so that the two tangential dipole components are output first followed by the field corresponding to the dipole aligned with the estimated cortex surface normal The orientation of the first two dipole components in the tangential plane is arbitrarily selected to create an orthogonal coordinate system noiseonly When creating a measurement fif file do not output a forward model file just the noise covariance matrix Senscov lt name gt Specifies the fif file containing a sensor covariance matrix to be included with the output If no other input files are specified only the covar
258. isual data Go back to the Manage averages dialog and switch all other conditions except the visual ones Observe the following 1 The left and right visual field responses are quite different in spatial distribution in the occipital area 2 There is a later response in the right parietal area almost identical to both visual stimuli Tip If you have the Neuromag software available the averaged data can be also viewed in the Neuromag data plotter xplotter See Section B 2 for instructions on how to use the Neuromag software at the MGH Marti nos Center 12 10 Computing the noise covariance matrix Another piece of information derived from the raw data file is the estimate for the noise covariance matrix which can be computed with the com mand mne process raw raw sample audvis raw fif lowpass 40 projon savecovtag cov cov audvis cov 307 12 The sample data set 308 12 11 12 11 1 Using the definitions in audvis cov this command will create the noise covariance matrix file sample audvis cov fif In this case the projections are set on The projection information is then attached to the noise covariance matrix and will be automatically loaded when the inverse operator decomposition 1s computed Tip You can study the contents of the covariance matrix computation description file audvis cov with help of Section 4 14 MEG MRI coordinate system alignment The mne_analyze module of the MNE is o
259. it2fiff utility has not been extensively tested yet Importing EEG data saved in the EDF EDF or BDF format 9 2 8 1 Overview The mne_edf2fiff allows conversion of EEG data from EDF EDF and BDF formats to the fif format Documentation for these three input for mats can be found at EDF http www edfplus info specs edf html EDF http www edfplus info specs edfplus html BDF http www biosemi com faq file_format htm EDF European Data Format and EDF are 16 bit formats while BDF is a 24 bit variant of this format used by the EEG systems manufactured by a company called BioSemi None of these formats support electrode location information and head shape digitization information Therefore this information has to be pro vided separately Presently hpts and elp file formats are supported to include digitization data For information on these formats see Section 9 3 1 and http www sourcesignal com formats_probe html Note that it is mandatory to have the three fiducial locations nasion and the two auricular points included in the digitization data Using the locations of the fiducial points the digitization data are converted to the MEG head coordinate system employed in the MNE software see Section 5 3 In the comparison of the channel names only the intial segment up to the first dash in the EDF EDF BDF channel name is significant The EDF files may contain an annotation channel which can be used to store trigg
260. ivalently that they are considered to be 30 times more noisy than their true noise value Since this implementation of channel selections requires recomputation of the initial guess candidate data discussed in Section 7 15 2 above changing the selection may take a finite amount of time especially if a BEM is used for the forward calculation Important Please note that when making a channel selection in the topo graphical displays the channels not present in a particular layout are also affected For example if you select channels in a layout showing the Vec torview planar gradiometers the magnetometer channels and EEG chan nels will be unselected 7 16 Coordinate frame alignment The MRI MEG coordinate frame alignment tools included in mne_analyze utilized the 3D digitizer Polhemus data acquired in the 192 MSH MNE Interactive analysis A beginning of each MEG EEG session and the scalp surface triangulation shown in the viewer window To access the coordinate frame alignment tools 1 Load digitizer data You can either load a data set containing digitizer information or load digitizer data from a file through the File Load dig itizer data menu choice 2 Set up the viewer window and make it visible see Section 7 10 The viewer options should be set to show the digitizer data see Section 7 10 2 3 Bring up the Adjust coordinate alignment dialog from Adjust Coordi nate alignment e268 X Adjust coordinate alignmen
261. ix In T terms of Section 6 2 3 UG data nchan x ntime The measured data One row contains the data at one time point The time points in the above matrix in seconds Number of averages as listed in the data file MSH MNE Table 9 3 The fields of Matlab structures 9 13 Converting raw data to Matlab format 9 13 1 The utility mne_raw2mat converts all or selected channels from a raw data file to a Matlab mat file In addition this utility can provide informa tion about the raw data file so that the raw data can be read directly from the original fif file using Matlab file I O routines Tip The MNE Matlab toolbox described in Chapter 10 provides direct access to raw fif files without a need for conversion to mat file format first Therefore it is recommended that you use the Matlab toolbox rather than mne_raw2mat which creates large files occupying disk space unnecessar ily Command line options mne_raw2mat accepts the following command line options 243 9 Data conversion 9 13 2 version Show the program version and compilation date help List the command line options raw lt name gt Specifies the name of the raw data fif file to convert mat lt name gt Specifies the name of the destination Matlab file info With this option present only information about the raw data file 1s included The raw data itself is omitted sel lt name gt Specifies a text file which contains the na
262. ke_cor_set if the input is in mgz or mgh format Hardcoded in software MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format Table 5 1 Coordinate transformations in FreeSurfer and MNE software packages The symbols T are defined in Figure 5 1 Note mne_make_cor_set mne_setup_mri prior to release 2 6 did not include transformations T T T_ and T in the fif files produced 96 MSH MNE The forward solution fal MSH MNE 5 3 The head and device coordinate systems Figure 5 2 The head coordinate system The MEG EEG head coordinate system employed in the MNE software is a right handed Cartesian coordinate system The direction of x axis is from left to right that of y axis to the front and the z axis thus points up The x axis of the head coordinate system passes through the two periau ricular or preauricular points digitized before acquiring the data with pos itive direction to the right The y axis passes through the nasion and is normal to the x axis The z axis points up according to the right hand rule and is normal to the xy plane The origin of the MEG device coordinate system is device dependent Its origin is located approximately at the center of a sphere which fits the occipital section of the MEG helmet best with x axis going from left to right and y axis pointing front The z axis is again normal to the xy plane with positive direction up Important The above definition is
263. ked_grad_amp Compute tangential gradient amplitudes from planar gradiometer data Table 10 14 Examples demostrating the use of the toolbox Important In order for the inverse operator calculation to work correctly with data processed with the Elekta Neuromag Maxfilter software the so called processing history block must be included in data files Previous versions of the MNE Matlab functions did not copy processing history to files saved As of March 30 2009 the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have been enchanced to include these data to the output file as appropriate If you have older raw data files created in Matlab from input which has been processed Maxfil ter it is necessary to copy the processing history block from the original to modified raw data file using the mne_copy_processing_history utility described in Section 11 4 8 The raw data processing programs mne_browse_raw and mne_process_raw have handled copying of the pro cessing history since revision 2 5 of the MNE software 10 2 Some data structures The MNE Matlab toolbox relies heavily on structures to organize the data This section gives detailed information about fields in the essential data structures employed in the MNE Matlab toolbox In the structure defini 260 MSH MNE The Matlab toolbox 10 MSH MNE tions data types referring to other MNE Matlab toolbox structures are shown in italics In addition Table 10 15 lists
264. l disturbances in software The section presents some relevant details of this method General concepts Unlike many other noise cancellation approaches SSP does not require additional reference sensors to record the disturbance fields Instead SSP relies on the fact that the magnetic field distributions generated by the sources in the brain have spatial distributions sufficiently different from those generated by external noise sources Furthermore it is implicitly 85 4 Processing raw data 86 assumed that the linear space spanned by the significant external noise patters has a low dimension Without loss of generality we can always decompose any n channel mea surement b into its signal and noise components as b t b b Further if we know that b t is well characterized by a few field patterns b b we can express the disturbance as b t Uc 1 e t where the columns of U constitute an orthonormal basis for b b c t is an m component column vector and the error term e t is small and does not exhibit any consistent spatial distributions over time i e C E fee I Subsequently we will call the column space of U the noise subspace The basic idea of SSP is that we can actually find a small basis set b b such that the conditions described above are satis m fied We can now construct the orthogonal complement operator T P I UU and apply it to b t yielding b t P b
265. l numbers as liste in the fi file ch_units nchan x 2 Units and unit multipliers as listed in the fif file The unit of the data is listed in the first column T 112 T m 201 V 107 At present the second column will be always zero i e no unit multiplier ch_pos nchan x 12 The location information for each channel The first three values specify the origin of the sensor coordinate system or the location of the elec trode For MEG channels the following nine number specify the x y and z direction unit vectors of the sensor coordinate system For EEG electrodes the first vector after the elec trode location specifies the location of the refer ence electrode If the reference is not specified this value is all zeroes The remaining unit vec tors are irrelevant for EEG electrodes Table 9 6 The fields of the raw data info structure 250 MSH MNE Data conversion wrote se eseiton ch_cals nchan x 2 The raw data output by mne_raw2mat are not calibrated The first column is the range mem ber of the fiff data structures and while the sec ond is the cal member To get calibrated data values in the units given in ch_units from the raw data the data must be multiplied with the product of range and cal meg_head_trans The coordinate frame transformation from the MEG device coordinates to the MEG head coordinates Table 9 6 The fields of the raw data info structure The raw data type 2 or 16 2 byte sign
266. laa blaa fwd lt name gt Specifies the name of the forward solution to use Senscov lt name gt Specifies the name of the noise covariance matrix to use If this file contains a projection operator attached by mne_browse_raw and mne_process_raw no additional projection vectors can be added with the proj option gradreg lt value gt Regularize the planar gradiometer section channels for which the unit of measurement is T m of the noise covariance matrix by the given amount The value is restricted to the range 0 1 For details see Section 6 2 4 magreg lt value gt Regularize the magnetometer and axial gradiometer section chan nels for which the unit of measurement is T of the noise covariance matrix by the given amount The value is restricted to the range 0 1 For details see Section 6 2 4 eegreg lt value gt Regularize the EEG section of the noise covariance matrix by the given amount The value is restricted to the range 0 1 For details see Section 6 2 4 diagnoise Omit the off diagonal terms from the noise covariance matrix in the computations This may be useful if the amount of signal free data has been insufficient to calculate a reliable estimate of the full noise covariance matrix Srccov lt name gt Specifies the name of the diagonal source covariance matrix to use By default the source covariance matrix is a multiple of the identity matrix This option can be employed to inco
267. lairach coordinates is that the linear MNI Talairach transform does matched the brains completely to the Talairach brain This is probably because the Talairach atlas brain is a rather odd shape and as a result it is difficult to match a standard brain to the atlas brain using an affine transform As a result the MNI brains are slightly larger in particular higher deeper and longer than the Talairach brain The differences are larger as you get further from the middle of the brain towards the outside The FreeSurfer Talairach coordinates mitigate this problem by additing a an additional transformation defined separately for negatice and positive MNI Talairach z coordinates These two transformations denoted by T_ and T in Figure 5 1 are fixed as discussed in http imaging mrc cbu cam ac uk imaging MniTalairach Approach 2 The different coordinate systems are related by coordinate transforma tions depicted in Figure 5 1 The arrows and coordinate transformation symbols T indicate the transformations actually present in the Free Surfer files Generally Xz xy Ry Riz Riz Xo X Yo Tp P1 21 22 823 Yol Pal Z3 zy R31 R32 R33 Zol Z l l 0 0 Od I l where x Yp and z are the location coordinates in two coordinate sys tems T is the coordinate transformation from coordinate system 1 to 2 Xo Yo and zo is the location of the origin of coordinate system 1 in coordinate system 2 and Ri are
268. lational operators lt gt lt gt and their textual equivalents lt gt eq le ge are available Table Table 11 5 gives some useful examples of source waveform expressions Fumenon Desenpton atan2 x y a y x nearest integer larger than x cosw x a b c cos shaped window centered at b witha rising slope of length a and a trailing slope of length b Table 11 4 Mathematical functions available for source waveform expressions MSH MNE Miscellaneous utilities deg x The value of x converted to from radians to degrees erf x l 2 f dt Largest integer value not larger than x modry 1 Ratio of the circumference of a circle and its diameter rand Gives a vector of uniformly distributed ran dom numbers from 0 to 1 Gives a vector of Gaussian random numbers distributed as N x y Note that if x and y rnorm x y are vectors each number generated will a different mean and variance according to the arguments shift x s Shifts the values in the input vector x by the number of positions given by s Note that s must be a scalar Table 11 4 Mathematical functions available for source waveform expressions MSH MNE 297 1 Miscellaneous utilities q 20e 9 sin 2 p1 10 x A 10 Hz sine wave with 20 nAm amplitude q 20e 9 sin 2 pi 2 x sin 2 pi 10 x A 10 Hz 20 nAm sine wave ampli tude modulated sinusoidally at 2 Hz q 20e 9 cosw t 100 100 100 2 cos
269. lay 0 000 eee 160 Selecting vertices eee 162 Defining viewing orientations 0 00 cee eee ees 163 Adjusting lighting sas sc eae ee owe woe oe Ree ed oe des 164 Producing output files tun ceeds dad eertekecetadss 165 Image output modes ee es 166 7 9 Morphing 455544 cece deca cceeeene cee deen sewe cea eee 167 MSH MNE 7 10 The viewer once access Bene hehe eee wae oe Re eee OVEIVIEW 1 0 ee ee ee eee Viewer ODIONS 3 anacekeu eeuexg eis aee ek eewoe dee basen 7 11 Magnetic field and electric potential maps OVCIVIEW nee 95424 sade w Paws 4 444 R Eee RE Ree raed os Technical description 0 0 0 eee ee ees Field mapping preferences 0 00 c cece eens 7 12 Working with current estimates 00000eeee Preferences 0 0 cc ee eee eas The SNR display lt se de04455655 25 eG nepeeeeed Se uee ess 7 13 Inquiring timecourses 0 0 ee Timecourses at vertices 0 0 00 ees Timecourses atlabels 0 0 00 eee es The timecourse manager 0 cee ee eee es Label timecourse files 2 00000 Creating new label files 0 0 0 0 ce eee eee TAG OVGHOVS enon cee auetea re eet ctuae nec eeae deve ve pees 7 15 Fitting current dipoles 0 00 cee ee Dipole fitting parameters 0 0 0 0 eee The dipole fitting algorithm 0 0 00 eee eee The dipole list 2 0 000 ees Channel select
270. le fiff_read_proj Read signal space projection data fiff_read_raw_segment Read a segment of raw data with time limits are specified in samples fiff read_raw_segment_times Read a segment of raw data with time limits specified in seconds fiff_setup_read_raw Set up data structures before using fiff_read_raw_segment or fiff_read_raw_segment_times Table 10 1 High level reading routines Seton Poe fiff_pick_channels Create a selector to pick desired channels from data according to include and exclude lists fiff_pick_channels_evoked Pick desired channels from evoked response data according to include and exclude lists fiff_pick_info Modify measurement info to include only selected chan nels fiff_pick_types Create a selector to pick desired channels from data according to channel types MEG EEG STIM in com bination with include and exclude lists fiff_pick_types_evoked Pick desired channels from evoked response data according to channel types MEG EEG STIM in com bination with include and exclude lists Table 10 2 Channel selection utilities 254 MSH MNE The Matlab toolbox 10 fiff_invert_transform Invert a coordinate transformation structure fiff_reset_ch_pos Reset channel position transformation to the default val ues present in the file fiff_transform_eeg_chs Transform electrode positions to another coordinate frame fiff_transform_meg_chs Apply a coordinate transformation to the sensor location
271. lectrode refer ence computation and identify bad channels Important It is strongly recommended that bad channels are identified and marked in the original raw data files If present in the raw data files the bad channel selections will be automatically transferred to averaged files noise covariance matrices forward solution files and inverse opera tor decompositions MSH MNE The Cookbook al 3 9 4 Downsampling the MEG EEG data MSH MNE 3 9 5 The minimum practical sampling frequency of the Vectorview system is 600 Hz Lower sampling frequencies are allowed but result in elevated noise level in the data It is advisable to lowpass filter and downsample the large raw data files often emerging in cognitive and patient studies to speed up subsequent processing This can be accomplished with the mne_process_raw and mne_browse_raw software modules For details see Sections 4 2 3 and 4 4 3 Tip It is recommended that the original raw file is called lt name gt _raw fif and the downsampled version lt name gt _ds_raw fif respectively Off line averaging The recommended tools for off line averaging are mne_browse_raw and mne_process_raw mne_browSe_raw is an interactive program for averag ing and noise covariance matrix computation It also includes routines for filtering so that the downsampling and filtering steps can be skipped Therefore with mne_browse_raw you can produce the off line average and noise covariance matrix est
272. list The timecourse shown in the MNE amplitude window is a compound measure of all timecourses within a label Two measures are available Average Compute the average over all label vertices at each time point Maximum Compute the maximum absolute value over all vertices at each time point If the data are signed the value is assigned the sign of the value at the maximum vertex This may make the timecourse jump from positive to negative abruptly if vertices with different signs are included in the label L2 norm sample by sample Compute the norm over the values in the vertices at each time point Pick vertex with largest L2 norm over time Compute the norm over time in each vertex and show the time course at the vertex with the largest norm 7 13 3 The timecourse manager The timecourse manager shown in Figure 7 23 has the following controls for each timecourse stored MSH MNE 181 Ea Interactive analysis 182 X Timecourse manager saved timecourses W o Color SAVE Forget vertex 71665 dSPM LA gt average go audvisO1_off tif af 2 Color SAVE Forget Vertex 75512 dSPM LA gt average go audvisO1_offlfit Ww 3 Color SAYE Forget vertex 85650 dSPM LA gt average go audvisO1_off fif EES fer A Figure 7 23 The timecourse manager Numbered checkbox Switches the display of this timecourse on and off Color This button shows the color of the timecourse curve The color ca
273. ll see above 281 1 Miscellaneous utilities 282 file lt name gt Specifies the name of the file to be modified Note You need write permission to the file to be processed 11 4 8 Copying the processing history In order for the inverse operator calculation to work correctly with data processed with the Elekta Neuromag Maxfilter software the so called processing history block must be included in data files Previous versions of the MNE Matlab functions did not copy processing history to files saved As of March 30 2009 the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have been enchanced to include these data to the output file as appropriate If you have older raw data files created in Matlab from input which has been processed Maxfil ter it is necessary to copy the processing history block from the original to modified raw data file using the mne_copy_processing_history utility described below The raw data processing programs mne_browse_raw and mne_process_raw have handled copying of the processing history since revision 2 5 of the MNE software mne_copy_processing_history is simple to use mne copy processing history from lt from gt to lt to gt where lt from gt is an original raw data file containing the processing his tory and lt to gt is a file output with older MNE Matlab routines Be care ful this operation cannot be undone If the lt from gt file does not have the process
274. ll be smoothed using this number of steps see Section 8 3 Opacity The range of this parameter is 0 1 The default value 1 means that the map overlaid on the cortical surface is completely opaque With lower opacities the color of the cortical surface will be visible to facilitate understanding the underlying folding pattern from the cur vature data displayed 7 12 2 The SNR display The SNR estimate display shows the SNR estimated from the whitened data in red and the apparent SNR inferred from the mismatch between the measured and predicted data in green The SNR estimate is computed from the whitened data x t related to the measured data x t by wo 0 a 2 a es l where C is the whitening operator introduced in Section 6 2 3 179 Ea Interactive analysis 180 7 13 7 13 1 7 13 2 The computation of the apparent SNR will be explained in future revi sions of this manual Inquiring timecourses Timecourses at vertices Timecourses at individual vertices can be inquired by clicking on a desired point on the surface with the left mouse button If the control key was down at the time of a click the timecourse will be added to the time course manager but left off With both control and shift down the time course will be added to the timecourse manager and switched on For more information on the timecourse manager see Section 7 13 3 The timecourses are be affected by the Retain sign and Retain normal
275. ll now fail Changes to existing software D 3 3 1 mne_add_patch_info e Changed option in to src and out to srcp e Added labeldir option D 3 3 2 mne_analyze New features include e The name of the digital trigger channel can be specified with the MNE_TRIGGER_CH_NAME environment variable e Using information from the fif data files the wall clock time corre sponding to the current file position is shown on the status line e mne_analyze can now be controlled by mne_browse_raw to facilitate interactive analysis of clinical data e Added compatibility with Elekta Neuromag Report Composer cliplab and improved the quality of hardcopies e Both in mne_browse_raw and in mne_analyze a non standard default layout can be set on a user by user basis see Section 4 5 6 e Added the digtrigmask option e Added new image rotation functionality using the mouse wheel or trackball 341 D Release notes 342 Added remote control of the FreeSurfer MRI viewer tkmedit see Section 7 18 Added fitting of single equivalent current dipoles and channel selec tions see Section 7 15 Added loading of FreeSurfer cortical parcellation data as labels Added support for using the FreeSurfer average brain fsaverage as a surrogate The surface selection dialog was redesigned for faster access to the files and to remove problems with a large number of subjects A shortcut button to direct a file selector to the appropriate default
276. lp of the 223 9 Data conversion 224 MNE_TRIGGER CH NAME environment variable when mne_browse_raw or mne_process_raw 1s invoked see Section 4 2 1 4 Only the two least significant bytes on the Status channel of BDF files are significant as trigger information the digtrigmask Oxff option MNE_TRIGGER CH MASK environment variable should be used to specify this to mne_browse_raw and mne_process_raw see Section 4 2 1 9 2 9 Importing EEG data saved in the Tufts University format The utility mne_tufts2fiff was created in collaboration with Phillip Hol comb and Annette Schmid from Tufts University to import their EEG data to the MNE software The Tufts EEG data is included in three files 1 The raw data file containing the acquired EEG data The name of this file ends with the suffix raw 2 The calibration raw data file This file contains known calibration sig nals and is required to bring the data to physical units The name of this file ends with the suffix c raw 3 The electrode location information file The name of this file ends with the suffix elp The utility mne_tufts2fiff has the following command line options version Show the program version and compilation date help List the command line options raw lt filename gt Specifies the name of the raw data file to process cal lt filename gt The name of the calibration data file If calibration data are missing the calibration coeff
277. lt value V gt Signal detection criterion for ECG channels stimIgnore lt time s gt Ignore this many seconds on both sides of the trigger when consid ering the epoch This parameter is useful for ignoring large stimulus artefacts e g from electrical somatosensory stimulation fixSkew Since the sampling of data and the stimulation devices are usually not synchronized all trigger input bits may not turn on at the same sample If this option is included in the off line averaging descrip tion file the following procedure is used to counteract this if there is a transition from zero to a nonzero value on the digital trigger channel at sample n the following sample will be checked for a transition from this nonzero value to another nonzero value If such an event pair is found the two events will be jointly considered as a transition from zero to the second non zero value With the fixSkew option mne_browse_raw mne_process_raw behaves like the Ele kta Neuromag on line averaging and Maxfilter software name lt fexf gt A descriptive name for this set of averages If the name contains multiple words enclose it in quotation marks like this The name will appear in the average manager window listing in the interactive version of the program and as a comment in the processed data sec tion in the output file 4 13 3 Category definition A category condition is defined by the parameters listed in this section eve
278. lue gt Specifies the number of averaged epochs in the input data If the input data file is one produced by mne_process_raw or mne_browse_raw the number of averages is correct in the file However if subtractions or some more complicated combinations of simple averages are produced e g by using the xplotter software the number of averages should be manually adjusted This is accom plished either by employing this flag or by adjusting the number of averages in the data file with help of mne_change_nave snr lt value gt An estimate for the amplitude SNR The regularization parameter will be setas A 1 SNR If the SNR option is absent the regular ization parameter will be estimated from the data The regulariza tion parameter will be then time dependent snronly Only estimate SNR and output the result into a file called SNR Each line of the file contains three values the time point in ms the estimated SNR 1 and the regularization parameter estimated from the data at this time point abs Calculate the absolute value of the current and the dSPM for fixed orientation data Spm Calculate the dSPM instead of the expected current value chi2 Calculate an approximate X statistic instead of the F statistic This is simply accomplished by multiplying the F statistic by three sqrtF Take the square root of the X or F statistic before outputting the stc file collapse Make all frames in the stc file or the wf
279. lysis 7 MSH MNE Tl neuromag sets or a transformation file stored from mne_analyze see Section 7 16 b Use EEG average electrode ref selects whether the average elec trode reference is applied to the data This is only available if the inverse operator is set to lt none gt c nave specifies the effective number of averages to compute the SNR correctly Usually your measurement file contains this information Load a new data set Filter Users mshidata GGi fit Directories Files subj1 ave fif subj1 cov fif test eeg meas cov fif l Ll Users msh data GG Users mshidata GG test eeg meas fwd fif visknow 1 cov fif visknow 1 noproj cov fif visknow 1 wide cov fif pa isknow 1 fif F aah m l al __ Available data sets 2 snobj gt average 3 repsnobj gt average 2 4 pseudo average 7 m Inverse operator lt none gt visknow3 7 eeg inv fif visknow3 7 eeg noproj iny fif 3 visknow3 7 meg eeg iny fif r m Options MRI head transform source lt Measurement gt Select W Use EEG average electrode ref nave enter 1 for auto R 4 Selection Usersimshidata GG visknow 1 fi OK Filter Cancel Help h Figure 7 8 The open dialog After the data set s has been selected the following actions will take place The inverse operator will be loaded Baselines will be ap
280. m pute the baseline values If either bmin or bmax is encoun tered previous baselines option will be ignored bmax lt value ms gt Upper limit of the baseline Data simulator Purpose The utility mne_simu creates simulated evoked response data for investi gation of the properties of the inverse solutions It computes MEG signals generated by dipoles normal to the cortical mantle at one or several ROIs defined with label files Colored noise can be added to the signals Command line options mne_simu has the following command line options version Show the program version and compilation date help List the command line options fwd lt name gt Specify a forward solution file to employ in the simulation label lt name gt Specify a label meg Provide MEG data in the output file 293 1 Miscellaneous utilities 294 11 13 3 eeg Provide EEG data in the output file out lt name gt Specify the output file By default this will be an evoked data file in the fif format raw Output the data as a raw data fif file instead of an evoked one mat Produce Matlab output of the simulated fields instead of the fif evoked file label lt name gt Define an ROI Several label files can be present By default the sources in the labels will have cos shaped non overlapping time courses see below timecourse lt name gt Explain the option here Sfreq lt freq Hz Explain th
281. m experiment to experiment depending on the number of electrodes used and the electrode cap configuration The utility mne_make_eeg_layout was created to produce custom EEG layout files based on the EEG electrode location information included in the channel description records mne_make_eeg_layout uses azimuthal equidistant projection to map the EEG channel locations onto a plane The mapping consists of the follow ing steps 1 A sphere is fitted to the electrode locations and the locations are trans lated by the location of the origin of the best fitting sphere 2 The spherical coordinates 7 0 and 0 corresponding to each trans lated electrode location are computed 3 The projected locations u RO cos and v RO_sing are com puted By default R 20 1m 2 i e at the equator 9 1 2 the multiplier is 20 This projection radius can be adjusted with the prad option Increasing or decreasing R makes the spacing between the channel viewports larger or smaller respectively 4 A viewport with width 5 and height 4 is placed centered at the pro jected location The width and height of the viewport can be adjusted with the width and height options The command line options are version Show the program version and compilation date help List the command line options lout lt name gt Specifies the name of the layout file to be output nofit Do not fit a sphere to the electrode locations but use a
282. mates are listed in text files The label files are pro duced by tksurfer or mne_analyze and specify regions of interests ROIs A label file name should end with lLh label for left hemisphere ROIs and with rh label for right hemisphere ones The corresponding output files are tagged with lh lt data type gt amp and rh lt data type gt amp respectively lt data type gt equals mne for expected current data and spm for dSPM data Each line of the output file contains the waveform of the output quantity at one of the source locations falling inside the ROI For more information about the label output formats see Section 7 13 3 1 139 6 The current estimates 140 6 5 9 labelcoords Include coordinates of the vertices in the output The coordinates will be listed in millimeters in the coordinate system which was specified for the forward model computations This option cannot be used with stc input files stcin because the stc files do not contain the coordinates of the vertices labelverts Include vertex numbers in the output The numbers refer to the com plete triangulation of the corresponding surface and are zero based The vertex numbers are by default on the first row or first column of the output file depending on whether or not the labeltimeby time option is present labeltimebytime Output the label data time by time instead of the default vertex by vertex output labeltag lt tag g
283. matrix derivation file 1s lt nrow gt lt ncol gt lt names of the input channels gt lt name gt lt weights gt The combination of the two arithmetic examples above can be thus repre sented as 2 3 EEG 002 EEG 003 EEG 010 EEG diff 1 1 0 EEG der 2 0 3 Before a derivation is accepted to use by mne_browse_raw the following criteria have to be met 1 All channels to be combined into a single derivation must have identi cal units of measure 2 All channels in a single derivation have to be of the same kind e g MEG channels or EEG channels 3 All channels specified in a derivation have to be present in the currently loaded data set The validity check is done when a derivation file is loaded into mne_browse_raw see Section 4 4 12 Tip You might consider renaming the EEG channels with descriptive labels related to the standard 10 20 system using the mne_rename_channels utility see Section 11 4 5 This allows you to use standard EEG channel names in the derivations you define as well as in the channel selection files used in mne_browse_raw see Section 4 5 5 MSH MNE Miscellaneous utilities 11 MSH MNE 11 6 Creating a custom EEG layout 11 6 1 Purpose Both MNE software mne_analyze and mne_browse_raw and Neuromag software xplotter and xfit employ text layout files to create topographical displays of MEG and EEG data While the MEG channel layout is fixed the EEG layout varies fro
284. ment File format png Portable Network Graphics format Important Only TIFF and RGB output routines are compiled into mne_analyze For other output formats to work the following programs must be present in your system tifftopdf tifftopnm pnmtojpeg and pnm topng There are three image saving modes which can be selected from the option menu labelled Output mode MSH MNE Interactive analysis 7 MSH MNE Single When OK is clicked one file containing the present image is output Snapshot A new image file is produced every time s is pressed in the image window see Sections 7 8 3 and 7 10 1 The image file name is used as the stem of the output files For example if the name is sam ple jpg the output files will be sample shot 001 jpg sample shot 002 jpg etc Automatic A new image file is produced every time the image window changes The image file name is used as the stem of the output files For example if the name is sample jpg the output files will be sample 001 jpg sample 002 jpg etc 7 9 Morphing The displayed surface distributions can be morphed to another subject s brain using the spherical morphing procedure see Chapter 8 In addition to the morphing surfaces loaded through File Load morphing surface surface patches for the same subject can be loaded through File Load morphing surface patch Switching between main and morphing sur faces 1s discussed in Section 7 8 3 Any labels displayed are
285. mes of the channels to include in the output file one channel name per line If the info option is specified sel does not have any effect fag lt tag gt By default all Matlab variables included in the output file start with MNE_ This option changes the prefix to lt tag gt _ Matlab data structures The Matlab files output by mne_raw2mat can contain two data structures lt tag gt _raw and lt tag gt _raw_info If info option is specifed the file contains the latter structure only The lt tag gt _raw stucture contains only one field data which is a matrix containing the raw data Each row of this matrix constitutes the data from one channel in the original file The data type of this matrix is the same of the original data 2 byte signed integer 4 byte signed integer or single precision float The fields of the lt tag gt _raw_info structure are listed in Table 9 4 Further explanation of the bufs field is provided in Table 9 5 wae se veseni orig_file string The name of the original fif file specified with the raw option Table 9 4 The fields of the raw data info structure 244 MSH MNE Data conversion wwrabe se oesonpton bufs nbuf x 4 This field is present if info option was specified on the command line For details see Table 9 5 highpass Highpass filter frequency Hz ch_names nchan string String array containing the names of the chan nels included ch_types nchan x 2 The
286. mes using the mne_rename_channels utility see Section 11 4 5 It is strongly rec ommended that you keep a copy of the channel alias file used by mne_rename_channels If necessary you can then easily return to the original channel names by running mne_rename_channels again with the revert option Load the data file into mne_browse_raw and use the interactive deriva tions editor to create the desired derived channels These are usually differences between the signals in two EEG electrodes Save the derivations from the file menu If desired move the derivations file to the standard location SHOME mne mne browse raw deriv fif Create new channel selections employing the original and derived channels using the channel selection tool described in Section 4 5 5 Save the new channel selections from the file menu If desired change the order of the channels in the selections in the selection file by editing it in a text editor and move it to the standard location SHOME mne mne_ browse raw sel MSH MNE Processing raw data 4 4 5 5 Selection Brings up a dialog to select channels to be shown in the main raw data dis play This dialog also allows modification of the set of channel selections as described below By default the available selections are defined by the file SMNE_ROOT share mne mne browse raw mne browse raw sel This default channel selection file can be modified by copying the file into SHOME m
287. meter 4004 Magnes reference gradi ometer measuring diago nal gradients 4005 Magnes reference gradi ometer measuring off diagonal gradients 4004 Magnes reference gradi ometer measuring diago nal gradients 5001 CTF 275 axial gradiometer CTF reference gradiome ter measuring diagonal gradients CTF reference gradiome ter measuring off diagonal gradients 0 0 0 0 0 0 mm 1 4 7 348 0 0 0 0 mm 1 8 3 674 6 364 0 0 mm 1 8 0 0 0 0 50 0 mm 1 4 7 348 0 0 50 0 mm 1 8 3 674 6 364 50 0 mm 1 8 20 20 0 0 mm 20 20 135 mm 87 5 20 0 0 mm 47 5 20 0 0 mm 87 5 20 0 0 mm 47 5 20 0 0 mm 20 20 0 0 mm 20 20 135 mm 0 0 0 0 0 0 mm 7 348 0 0 0 0 mm 3 674 6 364 0 0 mm 0 0 0 0 50 0 mm 7 348 0 0 50 0 mm 3 674 6 364 50 0 mm 8 6 8 6 0 0 mm 8 6 8 6 78 6 mm 47 8 8 5 0 0 mm 30 8 8 5 0 0 mm 47 8 8 5 0 0 mm 30 8 8 5 0 0 mm Table 5 3 Accurate coil descriptions 110 MSH MNE The forward solution u ommon Ja m fw MIT KIT system 0 0 0 0 0 0 mm axial gradiometer 6 328 0 0 0 0 mm 3 164 5 48 0 0 mm 0 0 0 0 50 0 mm 6 328 0 0 50 0 mm MSH MNE 3 164 5 48 50 0 mm Table 5 3 Accurate coil descriptions 5 8 4 The coil definition file The coil geometry information is stored in the text file MNE_ROOT share mne coil_def dat In this file any lines star
288. mplished by setting the SUBJECT environment variable surf Use the FreeSurfer surface files instead of the default ASCII trian culation files Please consult Section 3 6 1 for the standard file nam ing scheme noswap Traditionally the vertices of the triangles in tri files have been ordered so that seen from the outside of the triangulation the verti ces are ordered in clockwise fashion The fif files however employ the more standard convention with the vertices ordered counter clockwise Therefore mne_setup_forward_model by default reverses the vertex ordering before writing the fif file If for some reason you have counterclockwise ordered tri files available this behavior can be turned off by defining noswap When the fif file is created the vertex ordering is checked and the process is aborted if it is incorrect after taking into account the state of the swapping Should this happen try to run mne_setup_forward_model again including the noswap flag In particular if you employ the seglab software to create the triangulations see Appendix A the noswap flag is required This option is ignored if surf is specified ico lt number gt This option is relevant and required only with the surf option and if the surface files have been produced by the watershed algo rithm The watershed triangulations are isomorphic with an icosahe dron which has been recursively subdivided six times to yield 20480 t
289. mulus Response to right ear auditory stimulus Table 12 1 Trigger codes for the sample data set Setting up The sample data set is distributed with the MNE software as a compressed tar archive located at SMNE ROOT sample data MNE sample data tar gz To make a personal copy of the sample data set follow these steps 1 Set up for using the MNE software as instructed in Section 2 4 of this manual 2 Create a directory for your personal copy mkdir lt yourdir gt where lt yourdir gt 1s the location where you want your personal copy to reside Tho store the sample data set and to finish the tutorials in this Chapter you need approximately 600 MBytes of space on the disk where lt yourdir gt is located Go to your newly created sample data directory cd lt yourdir gt 4 Extract the sample data tar zxvf lt dir gt MNE sample data tar gz where lt dir gt is the location of the tar archive pro vided by your system administrator 09 To start the tutorials you need to 1 Set up MNE software user environment see Section 2 4 2 Set the SUBJECTS_DIR environment variable setenv SUBJECTS DIR lt yourdir gt subjects csh and tcsh or export SUBJECTS DIR lt yourdir gt subjects POSIX compat ible shell Most users at the Martinos Center have tcsh as their login Shell 3 Assign the SUBJECT environment variable the value sample MSH MNE The sample data set 12 MSH MNE 4 For convenience you can also
290. n be adjusted from the color editor which appears when the button is pressed Save Saves the timecourse If a single vertex is selected the time course file will contain some comment lines starting with the the percent sign one row of time point values in seconds and another with the data values The format of the timecourse data is explained in Section 7 13 3 1 below Forget Delete this timecourse from memory 7 13 3 1 Label timecourse files When timecourse corresponding to a label is saved the default is to save the displayed single timecourse in a format identical to the vertex time courses If Save all timecourses within the label is selected the Time by time output output changes the output to be listed time by time rather than vertex by vertex Include coordinates adds the vertex location information to the output file and Include vertex numbers adds the indices of picked vertices to the output see Figure 7 24 The vertex by vertex output for mats is summarized in Table 7 2 MSH MNE Interactive analysis ia pa pr a O ad n _ Save all timecourses within the label J Tirne by tirne output J Include coordinates Include vertex numbers selection ta sample dataMEG sample A1 lh spm tind yn Figure 7 24 Label timecourse saving options Comment lines beginning with oan b n u h ie Hx X z vy Table 7 2 Vertex by vertex output format n P is the number of vertices n is
291. n SSP please consult the references listed in Section 13 4 Covariance matrix of magnetometer data 19 a a 4g w 70 wm a Without SSP b With SSP Figure 4 16 An example of the effect of SSP The covariance matrix C of noise data on the 102 Vectorview magnetometers was computed a before and b after the application of SSP with three dimensional noise subspace The plotted quantity is _ C A Note that the vertical scale in b is ten times smaller than in a Estimation of the noise subspace As described above application of SSP requires the estimation of the sig nal vectors b b constituting the noise subspace The most common approach also implemented in mne_browse_raw is to compute a covari ance matrix of empty room data compute its eigenvalue decomposition and employ the eigenvectors corresponding to the highest eigenvalues as basis for the noise subspace It is also customary to use a separate set of vectors for magnetometers and gradiometers in the Vectorview system EEG average electrode reference In the computation of EEG based source estimates the MNE software employs the average electrode reference which means that the average over all electrode signals v Vy is subtracted from each v ee v Wok k It is easy to see that the above equation actually corresponds to the projec tion 87 4 Processing raw data v I uw v where 4 17 Covariance matrix estimation 4 17 1 88 T
292. n segmentation provided by FreeSurfer in the directory mri brain can be employed to create the inner skull surface triangulation with help of seglab the Neuromag MRI segmentation tool The descrip tion below assumes that the user is familiar with the seglab tool If neces sary consult the seglab manual Neuromag P N NM20420A A The data set mri brain typically contains tissues within or outside the skull in particular around the eyes These must be removed manually before the inner skull triangulation is created The editing and triangula tion can be accomplished as outlined below 1 Set up the MRIs for Neuromag software access Run the mne_setup_mri too as described in Section 3 4 As a result the directories mri T1l neuromag and mri brain neuromag are set up 2 Load the MRI data Open the file mri brain neuromag sets COR fif and adjust the scal ing of the data 3 Preparatory steps Set the minimum data value to using the min3D operator Make a backup of the data with the backup3D operator 4 Manual editing The maskDraw3D operation is recommended for manual editing To use it first employ the grow3D operator with threshold interval 2 255 and the seed point inside the brain Then do the editing in the slicer window as described in Section 5 4 2 of the seglab man MSH MNE Creating the BEM meshes A MSH MNE ual Note that it is enough to remove the connectivity to the extrace rebral tissues rather than erasing them c
293. name gt Specifies the output fif file containing the compensation channel weight matrix C see Section 9 2 4 The format of the text format compensation data file is lt number of MEG helmet channels gt lt number of compensation channels included gt lt cname gt lt cname gt lt name gt lt weights gt lt name gt lt weights gt In the above lt name gt denote names of MEG helmet channels and lt cname gt those of the compensation channels respectively If the chan nel names contain spaces they must be surrounded by quotes for exam ple MEG 0111 Importing KIT MEG system data The utility mne_kit2fiff was created in collaboration with Alec Maranz and Asaf Bachrach to import their MEG data acquired with the 160 channel KIT MEG system to MNE software To import the data the following input files are mandatory 1 The Polhemus data file elp file containing the locations of the fidu cials and the head position indicator HPI coils These data are usually given in the CTF 4D head coordinate system However mne_kit2fiff MSH MNE Data conversion EF MSH MNE does not rely on this assumption This file can be exported directly from the KIT system 2 A file containing the locations of the HPI coils in the MEG device coordinate system These data are used together with the elp file to establish the coordinate transformation between the head and device coordinate systems This file can be produced
294. nate frames see Section 7 16 MSH MNE 149 Ea Interactive analysis 7 4 3 The View menu The contents of the file menu is shown in Figure 7 4 p Show viewer show MRI viewer show coordinates show timecourse manager Figure 7 4 The View menu Show viewer Loads additional surfaces and pops up the viewer window The functions available in the viewer are discussed in Section 7 10 Show MRI viewer Bring up the tkmedit program to view MRI slices see Section 7 18 Show coordinates Show the coordinates of a vertex see Section 7 8 4 Show timecourse manager Brings up the timecourse manager if some timecourses are avail able Timecourses are discussed in Section 7 13 7 4 4 The Labels menu The contents of the Labels menu is shown in Figure 7 5 ROI analysis with help of labels is discussed in detail in Section 7 13 Load label Load all labels Load parcellation show label list Discard all labels Clear marked vertices Figure 7 5 The Labels menu The label menu contains the following items Load label Loads one label file for ROI analysis Load all labels Loads all label files available in a directory for ROI analysis 150 MSH MNE Interactive analysis 7 Load parcellation Load cortical parcellation data produced by FreeSurfer from direc tory SUBJECTS_DIR SUBJECT label and add the cortical regions defined to the label list Show label list Shows a li
295. nceueguebuus esse sbdwbeuceeesaneess 138 Label processing nos ch aeadeusbta deaene caehathon doa aes 139 Using stc file input 24264 Gn4 8eusden cea eade vee ee sees ae 140 6 6 Computing inverse from raw and evoked data 141 Command line options 0 00 cc ee ee 141 Implementation details 0 0 0 cee ees 144 Chapter 7 Interactive analysis 145 Fl OVEIVIOW so eeue oS pence ese eeeeees eee een eaaeeces 145 7 2 Command line options 0 cee ees 145 7 3 The main WINdOW 200 ee es 147 LA TNE MENUS 25 x 460e ese dere neteeee ken canwe tee eee 147 The File menu jc cc cgeess acu cues eee Gage eae Bae eee 147 The Adjust Menu 0 es 149 The View menu lt 2 2 seees stad d ou bed we ee eee eeadensd 150 The Labels menu 0 0 00 cece eee eee 150 The Dipoles menu 2140 26 000608 bebe Eda bce ewoeeeeed sd 151 The Help menu 4 saces atte toda d Ae eee es we oe es 151 7 9 Loading Gala 10 caase twee cde kkk eee eae oe ee ee oe 152 7 6 Loading epochs from a raw data file 154 7 7 Data displays 266 casos Sat tees gees en wees eek ae doe 155 The topographical display 0 0000 cee eee eee 155 The sample channel display n a anaana aaan 156 Scale settings nnana nannaa 156 7 8 The surface display 0 00 cece eee eee 158 The surface selection dialog 0 00 cece eens 159 The patch selection dialog 0 00 cee eee 160 Controlling the surface disp
296. ndicator coil locations cardinal landmarks EEG electrode locations and additional head surface points respectively Note that tkmedit does not recognize the fiducial as an alias for cardinal 22 9 Data conversion 228 lt identifier gt identifies the point The identifiers are usually sequential numbers For cardinal landmarks 1 left auricular point 2 nasion and 3 right auricular point For EEG electrodes identifier O signifies the reference electrode Some programs not tkmedit accept electrode labels as identifiers in the eeg category lt x mm gt lt y mm gt lt z mm gt Location of the point usually in the MEG head coordinate system see Section 5 3 Some programs have options to accept coordinates in meters instead of millimeters With meters option mne_transform_points lists the coordinates in meters 9 4 Converting volumetric data into an MRI overlay With help of the mne_volume_source_space utility Section 5 5 it is pos sible to create a source space which is defined within a volume rather than a surface If the mri option was used in mne_volume_source_space the source space file contains an interpolator matrix which performs a tri linear interpolation into the voxel space of the MRI volume specified At present the MNE software does not include facilities to compute volu metric source estimates However it is possible to calculate forward solu tions in the volumetric grid and use the MNE Ma
297. ne mne browse raw sel The format of this text file should be self explanatory x Selections Available selections Lefttemporal Right temporal Left parietal Right parietal Leftoccipital Fight occipital Left frontal Right frontal Figure 4 7 The channel selection dialog The channel selection dialog is shown in Figure 4 7 The number of items in the selection list depends on the contents of your selection file If the list has the keyboard focus you can easily move from one selection to another with the up and down arrow keys The two buttons below the channel selection buttons facilitate the modifi cation of the selections Add Brings up the selection dialog shown in Figure 4 8 to create new channel selections MSH MNE 59 4 Processing raw data 60 Omit current Delete the current channel selection Deletion only affects the selec tions in the memory of the program To save the changes perma nently into a file use Save channel selections in the File menu see Section 4 4 15 X Create a new selection Available channels MEG 0113 MEG 0112 MEG 0111 MEG 0122 MEG 0123 MEG 0121 MEG 0132 MEG 0133 MEG 0131 MEG 0143 MEG 0142 MEG 0141 MEG 0213 MEG 0212 MEG 0211 MEG 0222 MEG 0223 MEG 0221 MEG 0232 MEG 0233 MEG 0231 MEG 0243 MEG 0242 MEG 0241 MEG 0313 MEG 0312 MEG 0311 MEG 0322 MEG 0323 MEG 0321 Regexp i Name New selection Ll Select Add Done
298. ne option for the coordinate alignment It uses a triangulated scalp surface to facilitate the alignment Initial alignment Follow these steps to make an initial approximation for the coordinate alignment 1 Go to directory MEG sample 2 Launch mne_analyze 3 Select File Load digitizer data and load the digitizer data from sample audvis raw fif 4 Load an inflated surface for subject sample from File Load surface Bring up the viewer window from View Show viewer 6 Click Options in the viewer window Make the following selections a Switch left and right cortical surface display off b Make the scalp transparent c Switch Digitizer data on 4 After a while the digitizer points will be shown The color of the cir cles indicates whether the point is inside blue or outside red of the scalp The HPI coils are shown in green and the landmark locations in light blue or light red color The initial alignment is way off 5 Switch the Digitizer data off to get the big circles out of the way 6 Bring up the coordinate alignment window from Adjust Coordinate alignment 7 Click on the RAP Right Auricular Point button It turns red indicat ing that you should select the point from the viewer window Click at the approximate location of this point in the viewer The button jumps up turns to normal color and the MRI coordinates of the point appear in the text fields next to the button 8 Proceed similarly for
299. ne_annot2labels Convert parcellation data into label files see Section 11 14 mne_anonymize Remove subject specific information from a fif data file see Section 11 4 7 mne_average_forward_solutions Calculate an average of forward solutions see Section 5 10 mne_brain_vision2fiff Convert EEG data from Brain Vision format to fif format see Section 9 2 10 Table 2 2 Utility programs 12 MSH MNE Overview E a mne_change_baselines Change the dc offsets according to specifications given in a text file see Section 11 12 mne_change_nave Change the number of averages in an evoked response data file This is often necessary 1f the file was derived from sev eral files mne_check_eeg_locations Checks that the EEG electrode locations have been cor rectly transferred from the Polhemus data block to the channel information tags see Section 11 4 3 mne_check_surface Check the validity of a FreeSurfer surface file or one of the surfaces within a BEM file This program simply checks for topological errors in surface files mne_collect_transforms Collect coordinate transformations from several sources into a single fif file see Section 9 9 mne_compensate_data Change the applied software gradient compensation in an evoked response data file see Section 9 2 4 mne_convert_Ispcov Convert the LISP format noise covariance matrix output by graph into fif see Section 9 11 mne_convert_ncov Convert the ncov format noise covari
300. necessarily An exception to this is the case where you apply a filter to the data and save the band pass filtered epochs Command line options mne_epochs2mat accepts the following command line options are version Show the program version and compilation date MSH MNE Data conversion 9 help List the command line options raw lt name gt Specifies the name of the raw data fif file to use as input mat lt name gt Specifies the name of the destination file Anything following the last period in the file name will be removed before composing the output file name The binary epoch file will be called lt trimmed name gt epochs and the corresponding Matlab description file will be lt trimmed name gt desc mat tag lt tag gt By default all Matlab variables included in the description file start with MNE_ This option changes the prefix to lt tag gt _ events lt name gt The file containing the event definitions This can be a text or fif for mat file produced by mne_process_raw or mne_browse_raw see Section 4 10 5 With help of this file it is possible to select virtually any data segment from the raw data file If this option is missing the digital trigger channel in the raw data file or a fif format event file produced automatically by mne_process_raw or mne_browse_raw is consulted for event information event lt name gt Event number identifying the epochs of interest tmin lt time ms gt The
301. ning a list of currently defined events The list can be restricted to user defined events by checking User defined events only When an event is selected from the list the main display jumps to the corresponding time If a user 71 4 Processing raw data 4 10 3 12 defined event is selected it can be deleted with the Delete a user defined event button Loading and saving event files Using the Load Save events choices in the file menu events can be saved in text and fif formats see Section 4 10 5 below The loading dialogs have the following options Match comment with Only those events which will contain comments and in which the comment matches the entered text are loaded This filtering option is useful e g in loading averaging or covariance matrix computa tion log files see Sections 4 13 2 and page 81 If the word omit is entered as the filter only events corresponding to discarded epochs are loaded and the reason for rejection can be investigated in detail Add as user events Add the events as if they were user defined events As a result the annotation file saved next time mne_browse_raw closes this raw file will contain these events Keep existing events By default the events loaded will replace the currently defined ones With this option checked the loaded event will be merged with the currently existing ones The event saving dialogs have the following options controlling the data saved Save event
302. nner skull surface are automatically omitted The use of this option ensures that numerical inaccuracies for very superficial sources do not cause unexpected effects in the final current estimates Suitable value for this parame ter is of the order of the size of the triangles on the inner skull sur face If you employ the seglab software to create the triangulations this value should be about equal to the wish for the side length of the triangles MSH MNE The forward solution a mindistout lt name gt Specifies a file name to contain the coordinates of source space points omitted due to the mindist option mri lt name gt The name of the MRI description file containing the MEG MRI coordinate transformation This file was saved as part of the align ment procedure outlined in Section 3 10 These files typically reside in SSUBJECTS DIR S SUBJECT mri T1l neuromag sets trans lt name gt The name of a text file containing the 4 x 4 matrix for the coordinate transformation from head to mri coordinates With trans mri option is not required notrans The MEG MRI coordinate transformation is taken as the identity transformation i e the two coordinate systems are the same This option is useful only in special circumstances If more than one of the mri trans and notrans options are specified the last one remains in effect mricoord Do all computations in the MRI coordinate system The forward solution m
303. nsform_meg_chs and fiff_transform_eeg_chs eeg_loc double 6 The location of the EEG electrode in coord_frame coor dinates The first three values contain the location of the electrode m If six values are present the remaining ones indicate the location of the reference electrode for this channel coord_ frame int32 Initially the coordinate frame is FIFFV_COORD_DEVICE for MEG channels and FIFFV_COORD_HEAD for EEG channels unit int32 Unit of measurement Relevant values are 201 T m 112 T 107 V and 202 Am unit_mul int32 The data are given in units multiplied by 10 Presently unit_mul is always zero coil_def coildef The coil definition structure This is present only if mne_add_coil_defs has been successfully called Table 10 24 The ch structure 268 MSH MNE The Matlab toolbox kind wa het pa urine pre Sonea obe type of the projection item Possible values are listed in Table 10 15 Look for entries starting with FIFFV_PROJ_ITEM or FIFFV_MNE_PROJ_ITEM active int32 Is this item active i e applied or about to be applied to the data data named matrix The projection vectors The column names indicate the names of the channels associated to the elements of the vectors Table 10 25 The proj structure The kind of the compensation as stored in file ctfkind mapped into small integer numbers save_calibrated logical Were the compensation data saved in calibrated form If this field is
304. nt These correspond to the left and right hemisphere part of the source space respectively This source space data can be imported to MRIlab through the File Import Strings menu item exclude lt name gt Exclude the source space points defined by the given FreeSurfer label file from the output The name of the file should end with lh label if it refers to the left hemisphere and with rh label if it lists points in the right hemisphere respectively include lt name gt Include only the source space points defined by the given FreeSurfer label file to the output The file naming convention is the same as described above under the exclude option Are include labels are processed before the exclude labels all Include all nodes in the output files instead of only those active in the source space Note that the output files will be huge if this option is active 9 6 Listing BEM mesh data The utility mne_list_bem outputs the BEM meshes in text format The default output data contains the x y and z coordinates of the vertices listed in millimeters one vertex per line The command line options are version Show the program version and compilation date help List the command line options bem lt name gt The BEM file to be listed The file name normally ends with bem fif or bem soL fif out lt name gt The output file name MSH MNE Data conversion 9 MSH MNE id lt
305. nt lt number gt The zero time point of an epoch to be averaged is defined by a tran sition from zero to this number on the digital trigger channel The interpretation of the values on the trigger channel can be further modified by the ignore keyword ignore lt number gt If this parameter is specified the selected bits on trigger channel val ues can be mask set to zero out prior to checking for an existence of an event For example to ignore the values of trigger input lines three and eight specify ignore 132 2 2 132 delay lt time s gt Adds a delay to the time of the occurrence of an event Therefore if this parameter is positive the zero time point of the epoch will be later than the time of the event and correspondingly if the parame 19 4 Processing raw data 80 ter is negative the zero time point of the epoch will be earlier than the event By default there will be no delay tmin lt time s gt Beginning time point of the epoch tmax lt time s gt End time point of the epoch bmin lt time s gt Beginning time point of the baseline If both bmin and bmax parameters are present the baseline defined by this time range is subtracted from each epoch before they are added to the average basemin lt time s gt Synonym for bmin bmax lt time s gt End time point of the baseline basemax lt time s gt Synonym for bmax name lt text gt A descriptive name for this category
306. number gt Identify the surface to be listed The surfaces are numbered starting with the innermost surface Thus for a three layer model the surface numbers are 4 scalp 3 outer skull 1 inner skull Default value is 4 gdipoli List the surfaces in the format required by Thom Oostendorp s gdi poli program This is also the default input format for mne_surf2bem meters List the surface coordinates in meters instead of millimeters surf Write the output in the binary FreeSurfer format xfit Write a file compatible with xfit This is the same effect as using the options gdipoli and meters together 9 7 Converting surface data between different formats 9 7 1 The utility mne_convert_surface converts surface data files between dif ferent formats Important The MNE Matlab toolbox functions enable reading of Free Surfer surface files directly Therefore the mat option has been removed The dfs file format conversion functionality has been moved here from mne_convert_dfs Consequently mne_convert_dfs has been removed from MNE software command line options mne_convert_surface accepts the following command line options version Show the program version and compilation date help List the command line options fif lt name gt Specifies a fif format input file The first surface source space from this file will be read 231 9 Data conversion 232 tri lt name gt Specifies a
307. o accomplished by setting the SUBJECT environment variable Src lt name gt Source space name to use This option overrides the spacing option The source space is searched first from the current working directory and then from SSUBJECTS DIR lt subject gt bem The source space file must be specified exactly including the if exten sion Spacing lt spacing mm gt or ico lt number or oct lt number gt This is an alternate way to specify the name of the source space file For example if spacing 6 is given on the command line the source space files searched for are lt subject gt 6 src fif and SSUBJECTS DIR SSUBJECT bem lt subject gt 6 src fif The first file found is used Spacing defaults to 7 mm bem lt name gt Specifies the BEM to be used The name of the file can be any of lt name gt lt name gt bem fif lt name gt bem sol fif The file is searched for from the current working directory and from bem If MSH MNE The Cookbook al MSH MNE this option is omitted the most recent BEM file in the bem directory is used mri lt name gt The name of the MRI description file containing the MEG MRI coordinate transformation This file was saved as part of the align ment procedure outlined in Section 3 10 The file is searched for from the current working directory and from mri Tl neuro mag sets The search order for MEG MRI coordinate transforma tions is discussed below trans lt name gt T
308. o be shown Use full time range If this box is checked all data available in the data file will be shown Baseline min ms Specifies the lower time limit of the baseline Baseline max ms Specifies the upper time limit of the baseline Baseline in use Baseline subtraction can be switched on and off from this button MEG amp min fT cm Lower limit of the vertical scale of planar gradiometer MEG chan nels MEG amp max fT cm Upper limit of the vertical scale of planar gradiometer MEG chan nels MEG axmult cm The vertical scale of MEG magnetometers and axial gradiometers will be obtained by multiplying the planar gradiometer vertical scale limits by this value given in centimeters EEG amp min u V Lower limit of the vertical scale of EEG channels EEG amp max u V Upper limit of the vertical scale of EEG channels Show stimulus channel Show the digital trigger channel data in the sample view together with the sample channel MSH MNE 157 A Interactive analysis 158 fy fy fy K Scales Scale adjustment Analyze range min ms Analyze range max ms W Use full time range Baseline min ms ono Baseline max ms oo Baseline in use MEG amp min fTcm E1500 MEG amp max fT cm iso MEG axmult em 3 00 EEG amp min u Hoo EEG amp max u 10 0 J Show stimulus channel f_o Apply Cancel Help Figure 7 10 The Scales dialog 7 8 The surface display In mne_analyze the
309. o block Sfreq lt value Hz gt The sampling frequency of the data If this option is not specified the sampling frequency defaults to 1000 Hz lowpass lt value Hz gt The lowpass filter corner frequency used in the data acquisition If not specified this value defaults to 200 Hz highpass lt value Hz gt The highpass filter corner frequency used in the data acquisition If not specified this value defaults to 0 Hz DC recording out lt filename gt Specifies the name of the output fif format data file If this file is not specified no output is produced but the elp hpi and hsp files are processed normally MSH MNE Data conversion 9 MSH MNE 9 2 8 stim lt chs gt Specifies a colon separated list of numbers of channels to be used to synthesize a digital trigger channel These numbers refer to the scanning order channels as listed in the sns file starting from one The digital trigger channel will be the last channel in the file If this option is absent the output file will not contain a trigger channel stimthresh lt value gt The threshold value used when synthesizing the digital trigger chan nel see above Defaults to 1 0 add lt chs gt Specifies a colon separated list of numbers of channels to include between the 157 default MEG channels and the digital trigger chan nel These numbers refer to the scanning order channels as listed in the sns file starting from one Important The mne_k
310. o the cortex Optionally the current orientations can be fixed to be normal to the cortical mantle 2 The amplitudes of the currents have a Gaussian prior distribution with a known source covariance matrix 3 The measured data contain additive noise with a Gaussian distribution with a known covariance matrix The noise is not correlated over time The linear inverse operator The measured data in the source estimation procedure consists of MEG and EEG data recorded on a total of N channels The task is to estimate a total of M strengths of sources located on the cortical mantle If the num ber of source locations is P M P for fixed orientation sources and M 3P if the source orientations are unconstrained The regularized linear inverse operator following from the Bayesian approach is given by the Mx WN matrix al M R G GR G C 121 6 The current estimates 122 6 2 2 where G is the gain matrix relating the source strengths to the measured MEG EEG data C is the data noise covariance matrix and R is the source covariance matrix The dimensions of these matrices are NXM NxN and MxM respectively The x1 source strength vector is obtained by multiplying the N x 1 data vector by M The expected value of the current amplitudes at time f is then given by j t Mx t where x t is a vector containing the measured MEG and EEG data values at time t Regularization The a priori variance of the currents is in pr
311. odel name Default BEM model not set fl Unset Accurate field calculation Noise estimate Noise covariance lt not set a Unset J Omit off diagonal terms Regularization 0 0 Planar fixed fem 5 0 Axial fixed M 20 0 il EEG fixed uv 10 2 OK Cancel Help Figure 7 26 The dipole fitting preferences dialog 7 15 2 The dipole fitting algorithm When the dipole fitting preferences dialog is closed and the values have been modified the following preparatory calculations take place 188 MSH MNE Interactive analysis 7 MSH MNE ie If EEG data are included in fitting present the EEG sphere model spec ification corresponding to EEG sphere model name is loaded and scaled to the the EEG scalp radius If a boundary element model is used the additional data depending on the sensor locations are computed The noise covariance matrix is composed according to the specifica tions in the Dipole fitting preferences dialog The spatially whitened forward solution is computed in a grid of loca tions to establish the initial guess when a dipole is fitted Ifa BEM is in use the grid will be confined to the inner skull volume For a sphere model a spherical volume with an 80 mm radius centered at the sphere model origin will be employed The dipole grid will be rectan gular with a 10 mm spacing between the closest dipole locations Any locations closer th
312. of the bem files created by mne_prepare_bem_model see Section 5 7 If the BEM file contains a head surface triangulation it will be used instead of the one present in the bem lt subject gt head fif file Once all required surfaces have been loaded the viewer window shown in Figure 7 18 pops up In addition to the display canvas the viewer has Adjust view controls similar to the main surface display and options for graphics output The Adjust view controls do not have the option menu for standard viewpoints and has two additional buttons The output options only include graphics output as snapshots img or as movies mov Options This button pops up the viewer options window which controls the appearance of the viewer window Rescale This button adjusts the contour level spacing in the magnetic field and electric potential contour maps so that the number of contour lines is reasonable Reload Checks the modification dates of the surface files loaded to viewer and reloads the data if the files have been changed This is useful e g for display of different BEM tessellations The display can be also adjusted using keyboard shortcuts which are available once you click in the viewer display with the left mouse button Arrow keys Rotate the surface by increments specified in degrees in the Adjust View section als Enlarge the image Reduce the image Return to the default size r Rotate the image one full revolution
313. of triangles in use This is present only if the surface corresponds to a source space created with the ico option use_tris int32 nuse_tri The vertices of the triangles in use in the complete trian gulation This is present only if the surface corresponds to a source space created with the ico option nearest int32 np This field is present only if patch information has been computed for a source space For each vertex in the tri angulation these values indicate the nearest active source space vertex nearest_dist double np This field 1s present only if patch information has been computed for a source space For each vertex in the tri angulation these values indicate the distance to the near est active source space vertex Table 10 28 The surf structure Field Data type Description kind double What kind of a covariance matrix 1 noise covariance 2 source covariance dim int320 Dimension Dimension of the covariance matrix the Dimension of the covariance matrix matrix names cell Names of the channels associated with the entries may be empty Table 10 29 The cov structure MSH MNE 271 10 The Matlab toolbox data double dim dim The covariance matrix This a double dim vector for a diagonal covariance matrix proj The SSP vectors applied to these data cell Bad channel names Number of data points used to compute this matrix eig double dim The eigenvalues of the covariance
314. ographical display In both the sample channel display and the topographical display current time point can be selected with a left mouse click In addition time point of interest can be entered numerically in the text box at the bottom left corner of the main display The topographical display A selection of channels is always shown in the right most part of the main display The topographical layout to use is selected from Adjust Select trace layout which brings up a window with a list of available layouts The system wide layouts reside in MNE_ROOT share mne_analyze lout In addition any layout files residing in HOME mne lout are listed The format of the layout files and selection of the default layout is dis cussed in Section 4 5 6 Several actions can be performed with the mouse in the topographical data display Left button click Selects a time point of interest Left button click with control key Selects a time point of interest and selects the channel under the pointer to the sample channel display Left button drag with shift key Enlarges the view to contain only channels in the selected area 155 Ea Interactive analysis 156 7 7 2 7 7 3 Middle button click or drag Marks this channel as bad and clears all previously marked bad channel This action is only available if an inverse operator is not loaded An inverse operator dictates the selection of bad channels The current bad channel selection can b
315. olutions 0 0c eee ees 118 Purpose aacah oho esasdstesresectatdcasegbassaeaes ut 118 Command line options 0 0 eee 118 Chapter 6 The current estimates 121 6 1 Overview ne ccebeneceense tees seneseeeenseunecasee 121 6 2 Minimum norm estimates 0000 2 eee eee 121 The linear inverse operator 2 0000 eee eee 121 MeOUlANZauON 4 44envencaseeduea Kee teeeyeueseaetaeas 122 Whitening and scaling 0 000 cece eee eee 122 Regularization of the noise covariance matrix 123 Computation of the solution 000s 124 MSH MNE lil Noise normalization 0 000 eee eee eee ae 125 Predicted data nanana boat ef bbwen sede ds ou yess 126 Cortical patch statistics 0 0 eee eee 126 The orientation constraints 0 0000 eee eee eee 126 Depth weighting 2 2006 ccccliee Reeae wba ane ee ohn eee ne a aes 127 fMRl guided estimates 0 0 ee eee 127 6 3 Effective number of averages 000e eee eee 128 6 4 Inverse operator decomposition 2005 129 6 5 Producing movies and snapshots 0505 132 General Options n on nananana a ee eee 133 DUUINGGS sepr eee ne ia ween ee ee ape he dae eee en 133 Times and baseline 0 0 eee 133 Options controlling the estimates 0005 134 Visualization Options 2 0 0c ee 135 FAPESMONGING 4 a62teeee conned ds Gdateeteweceeneass 137 Output files 4 asb
316. ommand line options 00 cee eee 243 Matlab data structures 0 0 0 ee 244 Converting epochs to Matlab format 246 Command line options 0 cc eee 246 The binary epoch datafile 0 0 cee eee 249 Matlab data structures 0 0 0 0 cc ees 249 The Matlab toolbox 253 OvervieW soca dteudusew tone sd hed aeeceu sea seesn se cu 253 Some data structureS 2 02 c eee eee 260 On line documentation for individual routines 274 Miscellaneous utilities 275 Overview 1 eee ees 275 Finding software verSIONS 000 cee eee eee 275 Listing contents of afiffile 00 ce eee 275 Data file modification utilities 0 0008 276 Designating bad channels mne_mark_bad_channels 276 Fixing the encoding of the trigger channel mne_fix_stim14 277 Updating EEG location info mne_check_eeg_locations 277 Updating magnetometer coil types mne_fix_mag_coil_types 278 Modifying channel names and types mne_rename_channels 278 MSH MNE Modifying trigger channel data mne_add_triggers 280 PUIDOGe 6 4c4105d dna we boone ee sd be euanne aed oe euee ke 280 Command line options 2 00 0 eee 280 Removing identifying information 0000 eae 281 Copying the processing history 0 000 eee 282 11 5 Creating a derivation file 0 00 es 282 Purpose 4 g fac ote ee eee see eee oboe eee eee Ewha af
317. ompletely 5 Grow again and mask Once manual editing is complete employ the grow3D operator again and do mask3D with the backup data to see whether the result is satisfactory If not undo mask3D and continue manual editing Otherwise undo mask3D and proceed to the next step 6 Dilation It is advisable to make the inner skull surface slightly bigger than the brain envelope obtained in the previous step Therefore apply the dilate3D operation once or twice Use the values 1 for nbours and 26 for nhood in the first dilation and and 18 in the second one respectively 7 Triangulation Triangulate the resulting object with the triangulate3D operator Use a sidelength of 5 to 6 mm Check that the triangulation looks reasonable in the 3D viewing window 8 Save the triangulation Save the triangulated surface as a mesh into bem inner_skull tri Select unit of measure as millimeters and employ the MRI coordi nate system A 4 Using BrainSuite The BrainSuite software running under the Windows operating system can also be used for BEM mesh generation This software written by David W Shattuck is distributed as a collaborative project between the Laboratory of Neuro Imaging at the University of California Los Angeles Director Dr Arthur W Toga and the Biomedical Imaging Research Group at the University of Southern California Director Dr Richard M Leahy For further information see http brainsuite usc edu The conversion of
318. on changes the orientation so that the first two source components lie in the plane normal to the surface normal at the source location and the third component is aligned with it If patch information is available in the source space the nor mal is the average patch normal otherwise the vertex normal at the source location is used If the loose or loosevar option is employed surfsrc is implied exclude lt name gt Exclude the source space points defined by the given FreeSurfer label file from the source reconstruction This is accomplished by setting the corresponding entries in the source covariance matrix equal to zero The name of the file should end with lh label if it refers to the left hemisphere and with rh label if it lists points in the right hemisphere respectively proj lt name gt Include signal space projection SSP information from this file For information on SSP see Section 4 16 If the projections are present in the noise covariance matrix the proj option is not allowed Compute the inverse operator for surface current densities instead of the dipole source amplitudes This requires the computation of patch statistics for the source space Since this computation is time consuming it is recommended that the patch statistics are precom puted and the source space file containing the patch information 1s employed already when the forward solution is computed see Sec tions 3 5 and 3 11 For t
319. on to be applied to the data read from a dfs file to bring it to the same coordinate system as the MRI stack in the file frans lt name gt Specifies the name of a text file which contains the coordinate trans formation to be applied to the data read from the dfs file to bring it to the MRI coordinates see below This option is rarely needed flip By default the dfs surface nodes are assumed to be in a right ante rior superior RAS coordinate system with its origin at the left pos terior inferior LPI corner of the MRI stack Sometimes the dfs file has left and right flipped This option reverses this flip i e assumes the surface coordinate system is left anterior superior LAS with MSH MNE Data conversion EF its origin in the right posterior inferior RPI corner of the MRI stack Surfout lt name gt Specifies a FreeSurfer format output file fifout lt name gt Specifies a fif format output file triout lt name gt Specifies an ASCII output file that will contain the surface data in the triangle file format desribed in Section 5 6 3 pntout lt name gt Specifies a ASCII output file which will contain the vertex numbers only metersout With this option the ASCII output will list the vertex coordinates in meters instead of millimeters Swapout Defines the vertex ordering of ASCII triangle files to be output For details see Swap option above smfout lt name gt Specifies a smf
320. or Make a compensation matrix which switches the status of CTF software gradient compensation from one state to another mne_make_projector Create a signal space projection operator with the pro jection item definitions and cell arrays of channel names and bad channel names as input mne_make_projector_info Like mne_make_projector but uses the measurement info structure as input mne_set_current_comp Change the information about the compensation status in measurement info Table 10 8 Routines for software gradient compensation and signal space projection mne_pick_channels_cov Pick desired channels from a sensor covariance matrix mne_pick_channels_forward Pick desired channels rows from a forward solution mne_read_bem_surfaces Read triangular tessellations of surfaces for boundary element models mne_read_cov Read a covariance matrix mne_read_epoch Read an epoch of data from the output file of mne_epochs2mat mne_read_events Read an event list from a fif file produced by mne_browse_raw or mne_process_raw mne_read_forward_solution Read a forward solution from a fif file Read an inverse operator from a fif file Table 10 9 High level routines for reading MNE data files MSH MNE 257 10 The Matlab toolbox O ome o o o mne_read_morph_map Read an morphing map produced with mne_make_morph_maps see Section 8 4 mne_read_noise_cov Read a noise covariance matrix from a fif file mne_read_source_spaces Read source
321. origin Usually default value is appropriate For children it may be necessary to make this value smaller 7 12 Working with current estimates 7 12 1 Preferences The characteristics of the current estimates displayed are controlled from the MNE preferences dialog which pops up from Adjust Estimates This dialog shown in Figure 7 21 has the following controls SNR estimate This controls the regularization of the estimate 1 e the amount of allowed mismatch between the measured data and those predicted by the estimated current distribution Smaller SNR means larger allowed mismatch Typical range of SNR values is 1 7 As dis cussed in Section 6 2 the SNR value can be translated to the current variance values expressed in the source covariance matrix R This MSH MNE Interactive analysis 7 translation is presented as the equivalent current standard deviation value Show This radio button box selects the quantity to display MNE is the minimum norm estimate estimated value of the current dSPM is the noise normalized MNE and sLORETA is another version of the noise normalized solution which is claimed to have a smaller loca tion bias than the dSPM Mask with If MNE is selected in the Show radio button box it is possible to mask the solution with one of the statistical maps The masking map is thresholded at the value given in the Threshold text field and the MNE is only shown in areas with statistical values above this
322. ormations from the FreeSurfer data to the output file if possible For details see Section 9 8 D 3 3 12 mne_make_movie Added the noscalebar nocomments morphgrade rate and pick range options see Section 6 5 D 3 3 13 mne_make_source_space The spacing option is now implemented in this program which means mne_mris_trix is now obsolete The mne_setup_source_space script was modified accordingly Support for tri dec and dip files was dropped see Section 5 4 D 3 3 14 mne_mdip2stc This utility is obsolete and was removed from the distribution D 3 3 15 mne_project_raw This is utility is obsolete and was removed from the distribution The functionality is included in mne_process_raw MSH MNE Release notes D MSH MNE D 3 4 D 3 3 16 mne _rename channels Added the revert option see Section 11 4 5 D 3 3 17 mne_setup_forward_model Added the outershift and scalpshift options see Section 3 7 D 3 3 18 mne_simu Added source waveform expressions and the raw option see Section 11 13 D 3 3 19 mne_transform_points Removed the tomrivol option D 3 3 20 Matlab toolbox Several new functions were added see Chapter 10 Important The matlab function fiff_setup_read_raw has a significant change The sample numbers now take into account possible intial skip in the file i e the time between the start of the data acquisition and the start of saving the data to disk The first _samp member of t
323. oss different MEG studies 3 8 Setting up the MEG EEG analysis directory The remaining steps require that the actual MEG EEG data are available It is recommended that a new directory is created for the MEG EEG data processing The raw data files collected should not be copied there but rather referred to with symbolic links created with the 1n s command Averages calculated on line can be either copied or referred to with links MSH MNE The Cookbook a MSH MNE Tip If you don t know how to create a directory how to make symbolic links or how to copy files from the shell command line this is a perfect time to learn about this basic skills from other users or from a suitable ele mentary book before proceeding 3 9 Preprocessing the raw data 3 9 1 The following MEG and EEG data preprocessing steps are recommended 1 The coding problems on the trigger channel STI 014 may have to fixed see Section 3 9 1 2 EEG electrode location information and MEG coil types may need to be fixed see Section 3 9 2 3 The data may be optionally downsampled to facilitate subsequent pro cessing see Section 3 9 4 4 Bad channels in the MEG and EEG data must be identified see Section 3 9 3 5 The data has to be filtered to the desired passband If mne_browse_raw or mne_process_raw is employed to calculate the offline averages and covariance matrices this step is unnecessary since the data are filtered on the fly For information on t
324. ossible combinations have to be included 108 MSH MNE The forward solution u ommon Jo mm fw 47 8 8 5 0 0 mm 30 8 8 5 0 0 mm 47 8 8 5 0 0 mm 30 8 8 5 0 0 mm 6001 MIT KIT system 3 875 3 875 0 0 mm axial gradiometer 3 875 3 875 50 0 mm Table 5 2 Normal coil descriptions Note If a plus minus sign occurs in several coordinates all possible combinations have to be included u Descipton n mm fw 2 Neuromag 122 5 44 7 68 0 mm 1 4 16 54mm planar gradiometer 11 1 7 68 0 mm 3012 Vectorview type 5 89 6 71 0 3 mm 1 4 16 69mm a 10 8 6 71 0 3 mm 5 89 6 71 0 3 mm 1 4 16 69mm 10 8 6 71 0 3 mm 3022 Vectorview type 1 9 68 9 68 0 3 mm 1 16 magnetometer 9 68 3 23 0 3 mm 3 23 9 68 0 3 mm 3 23 3 23 0 3 mm 9 68 0 3 mm 1 16 3 23 0 3 mm 9 68 0 3 mm 3 23 0 3 mm CTF reference gradiome ter measuring off diagonal gradients 3013 Vectorview type 2 planar gradiometer 3023 Vectorview type 2 magnetometer 3024 Vectorview type 3 7 88 7 88 0 3 mm 1 16 magnetometer 7 88 2 63 0 3 mm 2 63 7 88 0 3 mm 2 63 2 63 0 3 mm 4001 Magnes WH magnetometer MSH MNE 0 0 0 0 0 0 mm 9 390 0 0 0 0 mm 4 695 8 132 0 0 mm Table 5 3 Accurate coil descriptions 1 4 1 8 1 8 109 The forward solution u Descipton n mm fw 4002 Magnes WH 3600 axial gradio
325. otations user defined events associated with it in mne_browse_raw information about them is automatically saved to an annotation file when a data file is closed i e when you quit mne_browse_raw or load a new data file This annotation file is called lt raw data file name without fif extension gt annot fif and will be stored in the same directory as the raw data file Therefore write permis sion to this directory is required to save the annotation file Both the events defined by the trigger channel and the user defined events have three properties 1 The time when the event occurred 2 The value on the trigger channel just before the change and now For user defined events the value before is always zero and the current value is user defined and does not necessarily reflect a change on the trigger channel The trigger channel events may also indicate changes between two non zero values and from a non zero to zero The event list described in Section 4 10 2 shows only transitions from zero to a non zero value Similarly the Jump to item in the tool bar described in Section 4 11 only detects transitions from zero to a nonzero value 3 An optional comment text which is especially helpful in associating user defined events with real world activity e g the subject closing or opening his her eyes or an epileptic patient showing indications of a seizure The event list The Windows Show event list menu choice shows a window contai
326. ough the Adjust Lights menu choice The col ors of the lights can be adjusted numerically or using a color adjustment dialog accessible through the Color buttons X Lights Light controls xpos y pos 2 Nos eapo po po ne fe fe C a a a a a a a a a a a a C a a a a a a a a a Se ee l OK Apply Cancel Help Figure 7 14 The lighting adjustment dialog MSH MNE Interactive analysis ZA 7 8 7 Producing output files Output w img no Figure 7 15 Graphics output controls Three types of output files can be produced from the main surface display using the graphics output buttons shown in Figure 7 15 w files w button These files are simple binary files which contain a list of vertex numbers on the cortical surface and their current data values The w files will be automatically tagged with Lh w and rh w They will only contain vertices which currently have a nonzero value Graphics snapshots img button These files will contain an exact copy of the image in tif or rgb for mats The output format and the output mode is selected from the image saving dialog shown in Figure 7 16 For more details see Section 7 8 8 If snapshot or automatic image saving mode is in effect thee img button terminates this mode QuickTime movies mov button These files will contain a sequence of images as a QuickTime movie file The movie saving dialog shown in Figure 7 17 specifies the time range and the
327. ow size and the page up and down or control up and down cursor keys one window size Remove dc Remove the dc offset from the signals for display This does not affect the data used for averaging and noise covariance matrix esti mation Keep dc Return to the original true dc levels Jump to Enter a value of a trigger to be searched for The arrow buttons jump to the next event of this kind A selection is also automatically cre ated and displayed as requested in the scales dialog see Section 4 5 2 If the button is active previous selections are kept otherwise they are cleared Picked to Make user events with this event number at all picked time points It is also possible to add annotated user events with help of the annota tion dialog For further information see Section 4 10 Forget Forget desired user events Average Compute an average to this event The tool bar status line shows the starting time and the length of the win dow in seconds as well as the cursor time point The dates and times in parenthesis show the corresponding wall clock times in the time zone where mne_browse_raw is run Note The wall clock times shown are based on the information in the fif file and may be offset from the true acquisition time by about 1 second This offset is constant throughout the file The times reflect the time zone setting of the computer used to analyze the data rather than the one use to acquire them 19
328. p 245 59 1999 13 4 Signal space projections C D Tesche M A Uusitalo R J IlImoniemi M Huotilainen M Kajola and O Salonen Signal space projections of MEG data characterize both distributed and well localized neuronal sources Electroencephalogr Clin Neurophysiol vol 95 pp 189 200 1995 M A Uusitalo and R J Ilmoniemi Signal space projection method for separating MEG or EEG into components Med Biol Eng Comput vol 35 pp 135 40 1997 13 5 Minimum norm estimates M H m l inen and R Ilmoniemi Interpreting magnetic fields of the brain minimum norm estimates Helsinki University of Technology Espoo TKK F A559 1984 A Dale and M Sereno Improved localization of cortical activity by combining EEG and MEG with MRI cortical surface reconstruction A linear approach J Cog Neurosci vol 5 pp 162 176 1993 M S H m l inen and R J Ilmoniemi Interpreting magnetic fields of the brain minimum norm estimates Med Biol Eng Comput vol 32 pp 35 42 1994 A M Dale A K Liu B R Fischl R L Buckner J W Belliveau J D Lewine and E Halgren Dynamic statistical parametric mapping com MSH MNE Useful reading 13 MSH MNE bining fMRI and MEG for high resolution imaging of cortical activity Neuron vol 26 pp 55 67 2000 A K Liu A M Dale and J W Belliveau Monte Carlo simulation stud ies of EEG and MEG localization accuracy Hum Brain Mapp vol 16
329. pace exits with an error morph lt name gt Name of a subject in SUBJECTS_DIR If this option is present the source space will be first constructed for the subject defined by the subject option or the SUBJECT environment variable and then morphed to this subject This option is useful if you want to create a source spaces for several subjects and want to directly compare the data across subjects at the source space vertices without any mor phing procedure afterwards The drawback of this approach is that the spacing between source locations in the morph subject is not going to be as uniform as it would be without morphing surf lt namel gt lt name2 gt FreeSurfer surface file names specifying the source surfaces sepa rated by colons Spacing lt spacing mm gt Specifies the approximate grid spacing of the source space in mm ico lt number gt Instead of using the traditional method for cortical surface decima tion it is possible to create the source space using the topology of a recursively subdivided icosahedron lt number gt gt 0 or an octahe dron lt number gt lt 0 This method uses the cortical surface inflated to a sphere as a tool to find the appropriate vertices for the source space The benefit of the ico option is that the source space will have triangulation information between the decimated vertices included which some future versions of MNE software may be able to utilize The number of
330. plied as specified in the scales dialog 3 Projection will be applied to the data If no inverse operator is speci fied the source for the projection data will be the data file and the aver age EEG reference setting in the options If an inverse operator is included the projection will be read from the data file 4 If an inverse operator is loaded whitened data will be computed N e 153 Ea Interactive analysis 154 5 If an inverse operator is loaded the SNR estimate as well as the effec tive SNR will be computed from the whitened data and displayed in the SNR window 6 Waveforms will be shown in the topographical display as well as in the sample channel display If multiple data sets are loaded each data set has the following individual settings Amplitude and time scale settings Baseline Picked time point Sample channel to be displayed and MNE display preferences see Section 7 12 1 MBBWwWN If a data set has not been previously displayed the currently active set tings are copied to the data set Tip If you double click on an inverse operator file name displayed in the Inverse operator list the command used to produced this file will be dis played in a message dialog 7 6 Loading epochs from a raw data file Instead of an evoked response data file it is possible to load epochs of data single trials from a raw data file This option is invoked from File Open raw The file selection
331. point in one of the input stc files is reached integ lt At ms gt Integration time for each frame Defaults to zero The integration will be performed on sensor data If the time specified for a frame is to the integration range will be t At 2 lt t lt t At 2 ste lt filename gt Specifies an input stc file The filename can be specified with one of the 1h stc and rh stc endings or without them This phrase ends the present context and starts an input context deststc lt filename gt Specifies the output stc file The filename can be specified with one of the lh stc and rh stc endings or without them This phrase ends the present context and starts the output context lh Process the left hemisphere By default both hemispheres are pro cessed rh Process the left hemisphere By default both hemispheres are pro cessed The contextual phrases are weight lt value gt Specifies the weight of the current data set This phrase is valid in the input and output contexts abs Specifies that the absolute value of the data should be taken Valid in all contexts If specified in the global context applies to all subse quent input and output contexts If specified in the input or output contexts applies only to the data associated with that context 209 8 Morphing and averaging 210 pow lt value gt Specifies that the data should raised to the specified power For neg ative values the absolute valu
332. presentation available The standard or normal representation see Table 5 2 3 The most accurate representation available see Table 5 3 Table 5 5 Coil representation accuracies Each coil description line is followed by one or more integration point lines consisting of seven numbers lt weight gt Gives the weight for this integration point last column in Tables 5 2 and 5 3 lt x m gt lt y m gt lt z m gt Indicates the location of the integration point fourth column in Tables 5 2 and 5 3 lt nx gt lt ny gt lt nz gt Components of a unit vector indicating the field component to be selected Note that listing a separate unit vector for each integration points allows the implementation of curved coils and coils with the gradiometer loops tilted with respect to each other MSH MNE The forward solution al MSH MNE 5 8 5 5 9 5 9 1 5 9 2 Creating the coil definition file The standard coil definition file MNE ROOT share mne coil_def dat is included with the MNE software package The coil definition file can be recreated with the utility mne_list_coil_def as follows mne_list_coil_ def out MNE_ROOT share mne coil_def dat Computing the forward solution Purpose Instead of using the convenience script mne_do_forward_solution it 1s also possible to invoke the forward solution computation program mne_forward_solution directly In this approach the convenience of the automatic file naming
333. process_raw specify the desired compensation grade and save a new raw data file Importing Magnes compensation channel data At present it is not possible to include reference channel data to fif files containing 4D Magnes data directly using the conversion utilities avail able for the Magnes systems However it is possible to export the com MSH MNE Data conversion 9 pensation channel signals in text format and merge them with the MEG helmet channel data using mne_insert_4D_comp This utility has the fol lowing command line options yersion Show the program version and compilation date help List the command line options In lt name gt Specifies the input fif file containing the helmet sensor data out lt name gt Specifies the output fif file which will contain both the helmet sen sor data and the compensation channel data ref lt name gt Specifies a text file containing the reference sensor data Each line of the reference sensor data file contains the following informa tion epoch is always one time s time point of this sample data T the reference channel data values The standard locations of the MEG helmet and compensation sensors in a Magnes WH3600 system are listed in SMNE ROOT share mne Magnes WH3600 pos mne_insert_4D_comp matches the helmet sen sor positions in this file with those present in the input data file and trans forms the standard compensation channel locations accordin
334. ps J Keep previous dipoles Done Show Save Clear Help Figure 7 27 The dipole list The dipole list dialog shown in Figure 7 27 contains the parameters of the dipoles fitted In addition it is possible to import current dipole locations from the Neuromag source modelling program xfit to mne_analyze Dipoles can be imported in two ways 190 MSH MNE Interactive analysis A MSH MNE 1 Bring up the dipole list window from Windows Show dipole list Drag and drop selected dipoles from one of the xfit dipole list to this list using the middle mouse button 2 Drag and drop dipoles from one of the xfit dipole lists over the main surface display The dipole list will appear and contain the dropped dipoles The buttons at the bottom of the dialog perform the following functions Done Hide the dialog Show Show the currently selected dipoles as specified in Display options see below Save Save the selected or all dipoles If the file name specified in the file selection dialog that pops up ends with bdip the dipole data will be saved in the binary bdip format compatible with the Neuromag xfit software otherwise a text format out put will be used In the text file comments will be included on lines starting with the percent sign so that the text format can be easily loaded into Matlab Clear Clear the selected dipoles from the list When you double click on one of the dipoles or select several dipoles an
335. purpose 3 Installation and Maintenance You are solely responsible for installing and maintaining the Software and for testing the Software for proper operation Licensor shall have no obligation to provide any support maintenance corrections debugging improvements modifications upgrades or updates of the Software or notice of any of the forgoing or 349 E Licence agreement 350 otherwise assist Licensee in installing configuring integrating under standing or using the Software 4 Attributions and Acknowledgments You must preserve and maintain all applicable attributions copyright notices and licenses included in or applicable to the Software You agree to provide acknowledgement of Licensor and its designated professional staff who participated in the creation of the Software in publications or presentations in accordance with standard academic practice provided that you may not otherwise use Licensor s name logos or trademarks or the name of any individual associated with Licensor or of any funding agency in any advertising promotional or sales material or publicity or in any document employed to obtain funds or financing or to endorse or promote any research results or products related to or arising from the Software without the prior written consent of a person authorized to make such consent Third Party Software This Agreement does not grant any rights with respect to any third party software except tho
336. quence of tokens separated by whitespace space tab or newline If a token con sists of several words it has to be enclosed in quotes One or more tokens constitute an phrase which has a meaning for the averaging definition Any line starting with the pound sign is a considered to be a comment line There are two kinds of phrases in the description file global and con textual The global phrases have the same meaning independent on their location in the file while the contextual phrases have different effects depending on their location in the file There are three types of contexts in the description file the global context an input context and the output context In the beginning of the file the context is global for defining global parameters The input context defines one of the input files subjects while the output context specifies the des tination for the average MSH MNE Morphing and averaging 8 MSH MNE The global phrases are tmin lt value ms gt The minimum time to be considered The output stc file starts at this time point 1f the time ranges of the stc files include this time Other wise the output starts from the next later available time point tstep lt step ms gt Time step between consecutive movie frames specified in millisec onds tmax lt value ms gt The maximum time point to be considered A multiple of tstep will be added to the first time point selected until this value or the last time
337. quire timecourses of vertices and labels from dynamic stc cortical overlays in the same way as from original data and store the results in text files If a static overlay w file or a scalp overlay is selected the timecourses are picked from the data loaded if available 7 15 Fitting current dipoles 7 15 1 Starting from MNE software version 2 6 mne_analyze includes routines for fitting current dipoles to the data At present mne_analyze is limited to fitting single equivalent current dipole ECD at one time point The parameters affecting the dipole fitting procedure are described in Section 7 15 1 The results are shown in the dipole list Section 7 15 3 The selection of channels included can be adjusted interactively or by pre defined selections as described in Section 7 15 4 Warning The current dipole fitting has been added recently and has not been tested comprehensively Especially fitting dipoles to EEG data may be unreliable Dipole fitting parameters Prior to fitting current dipoles the fitting parameters must be set with the Dipole fitting preferences dialog shown in Figure 7 26 The dialog is brought up from the Setup fitting choice in the Dipoles menu This dia log contains three sections Forward model Modalities and Noise esti mate The Forward model section specifies the forward model to be used Sphere model origin x y z mm Specifies the origin of the spherically symmetric conductor model in MEG EEG h
338. r the BEM basis functions are linear functions on each triangle and the collocation points are the vertices of the triangula MSH MNE The forward solution al MSH MNE tion This is the preferred method to use The accuracy will be the same or better than in the constant collocation approach with about half the number of unknowns in the BEM equations 5 8 Coil geometry information 5 8 1 This Section explains the presentation of MEG detection coil geometry information the approximations used for different detection coils in MNE software Two pieces of information are needed to characterize the detec tors 1 The location and orientation a local coordinate system for each detec tor 2 A unique identifier which has an one to one correspondence to the geometrical description of the coil The sensor coordinate system The sensor coordinate system is completely characterized by the location of its origin and the direction cosines of three orthogonal unit vectors pointing to the directions of the x y and z axis In fact the unit vectors contain redundant information because the orientation can be uniquely defined with three angles The measurement fif files list these data in MEG device coordinates Transformation to the MEG head coordinate frame can be easily accomplished by applying the device to head coordi nate transformation matrix available in the data files provided that the head position indicator was used Optionally t
339. r nasion to indicate a fiducial landmark or any word which is not a name of any channel in the data If lt name gt is a name of an EEG channel available in the data the location is included in the Polhemus data as an EEG electrode locations and inserted as the loca tion of the EEG electrode If the name is one of the fiducial landmark names the point is included in the Polhemus data as a fiducial landmark Otherwise the point is included as an additional head surface points The standard eeg file produced by CTF software does not contain the fiducial locations If desired they can be manually copied from the pos file which was the source of the eeg file Note In newer CTF data the EEG position information maybe present in the res4 file If the eeg file is present the positions given there take pre cedence over the information in the res4 file Important mne_ctf 2fiff converts both epoch mode and continuous raw data file into raw data fif files It is not advisable to use epoch mode files with time gaps between the epochs because the data will be discontinuous in the resulting fif file with jumps at the junctions between epochs These 213 9 Data conversion 214 9 2 3 discontinuities produce artefacts if the raw data is filtered in mne_browse_raw mne_process_raw or graph Note The conversion process includes a transformation from the CTF head coordinate system convention to that used in the Neuromag systems Importing C
340. r of the size of the triangles on the inner skull sur face If you employ the seglab software to create the triangulations this value should be about equal to the wish for the side length of the triangles megonly Omit EEG forward calculations 33 al The Cookbook 34 eegonly Omit MEG forward calculations all Compute the forward solution for all vertices on the source space overwrite Overwrite the possibly existing forward model file help Show usage information for the script The MEG MRI transformation is determined by the following search sequence 1 If the mri option was present the file is looked for literally as spec ified in the directory of the measurement file specified with the meas option and in the directory SUBJECTS_DIR SUBJECT mri T1 neuromag sets If the file is not found the script exits with an error message 2 If the trans option was present the file is looked up literally as specified If the file is not found the script exists with an error mes sage 3 If neither mri nor trans option was not present the following default search sequence is engaged a The 1f ending in the measurement file name is replaced by trans f1if If this file is present it will be used b The newest file whose name ends with trans fif in the direc tory of the measurement file is looked up If such a file is present it will be used c The newest file whose name starts with
341. r the amplitude SNR The regularization parameter will be set as A 1 SNR The default value is SNR 3 Auto matic selection of the regularization parameter is currently not sup ported Spm Calculate the dSPM instead of the expected current value SLORETA Calculate the noise normalized estimate using the sLORETA approach SLORETA solutions have in general a smaller location bias than either the expected current MNE or the dSPM Signed Indicate the current direction with respect to the cortex outer normal by sign Currents flowing out of the cortex are thus considered posi tive warm colors and currents flowing into the cortex negative cold colors picknormalcomp The components of the estimates corresponding to directions tan gential with the cortical mantle are zeroed out 6 5 5 Visualization options subject lt subject gt Specifies the subject whose MRI data is employed in the visualiza tion This must be the same subject that was used for computing the current estimates The environment variable SUBJECTS_DIR must be set to point to a locations where the subjects are to be found morph lt subject gt Morph the data to to the cortical surface of another subject The Quicktime movie stc file graphics snapshot and w file outputs are affected by this option i e they will take the morphing into account and will represent the data on the cortical surface of the subject defined with this option The st
342. radiuses will be in ascending order and the radius of the outermost layer is scaled to 1 0 The scalp radius specified with the eegrad option is then consulted to scale the model to the correct dimensions Even if the model setup file is MSH MNE The forward solution MSH MNE 5 9 5 5 9 6 not present a model called Default is always provided This model has the structure given in Table 5 6 Relative outer C sa po Table 5 6 Structure of the default EEG model EEG forward solution in the sphere model When the sphere model is employed the computation of the EEG solution can be substantially accelerated by using approximation methods described by Mosher Zhang and Berg see Section 13 3 Mosher et al and references therein mne_forward_solution approximates the solution with three dipoles in a homogeneous sphere whose locations and ampli tudes are determined by minimizing the cost function SCs ees Pe p S O aa scalp where r 7 and Uj U are the locations and amplitudes of the approximating dipoles and V ue and Vaor Ale the potential distribu tions given by the true and approximative formulas respectively It can be shown that this integral can be expressed in closed form using an expan sion of the potentials in spherical harmonics The formula is evaluated for the most superficial dipoles i e those lying just inside the inner skull sur face Field derivatives If the grad option is speci
343. reasonable solution unless and initial alignment is performed first according to Section 12 11 1 Outlier points should be excluded as described above No attempt is made to compensate for the possible distance of the digitized EEG electrode locations from the scalp Saving the transformation To create a MRI fif description file which incorporates the coordinate transformation click Save MRI set in the Adjust coordinate alignment dia log This will create the MRI set file in the SSUBJECTS DIR sample mri Tl neuromag sets directory which was created by mne_setup_mri_data see Section 12 5 1 The file will be called COR lt username gt lt date gt lt time gt fit where lt username gt is your login name You can also save transformation to a fif file through the Save button If the file does not exist it will only contain the coordinate transformation If the file exists it will be inserted to the appropriate context An existing transformation will not be replaced unless Overwrite existing transform 1s checked in the save dialog Once you have saved the coordinate transformation press Done and quit mne_analyze File Quit Important If you dismiss the alignment dialog before saving the trans formation it will be lost The forward solution To compute the forward solution say cd SSAMPLE MEG sample mne do forward solution mindist 5 MSH MNE The sample data set 12 MSH MNE spacing oct 6 bem sample 5120
344. rences where w 1 or w l i 1 n we have n I Log gt IL i Inverse operator decomposition The program mne_inverse_operator calculates the decomposition A GR UAV described in Section 6 2 5 It is normally invoked from the convenience script mne do inverse operator This sec tion describes the options to mne inverse operator should a user need to invoke it directly for special purpose processing The command line options of mne inverse operator are version Show the program version and compilation date help List the command line options meg Employ MEG data in the calculation of the estimates eeg Employ EEG data in the calculation of the estimates Note The EEG computations have not been throughly tested at this time fixed Use fixed source orientations normal to the cortical mantle By default the source orientations are not constrained 129 6 The current estimates 130 loose lt amount gt Employ a loose orientation constraint LOC This means that the source covariance matrix entries corresponding to the current com ponent normal to the cortex are set equal to one and the transverse components are set to lt amount gt Recommended value of amount is 0 2 0 6 loosevar lt amount gt Use an adaptive loose orientation constraint This option can be only employed if the source spaces included in the forward solution have the patch information computed see Section 3 5 B
345. rface or File Load morphing surface is invoked the surface selection dialog shown in Figure 7 11 appears AAD x Load a surface Available subjects sample available surfaces 3 orig pial smoothwm sphere sphere reg white Fi selected surface inflated x rotation deg oo k y rotation deg 0 0 z rotation deg i morph sample OK Cancel Help Figure 7 11 The surface selection dialog The dialog has the following components List of subjects This list contains the subjects available in the directory set with the SUBJECTS DIR environment variable List of available surfaces for the selected subject Lists the surfaces available for the current subject When you click on an item in this list it appears in the Selected surface text field x rotation deg Specifies the initial rotation of the surface around the x left to right axis Positive angle means a counterclockwise rotation when the surface is looked at from the direction of the positive x axis Some times a more pleasing visualization is obtained when this rotations are specified when the surface is loaded MSH MNE 159 A Interactive analysis y rotation deg Specifies the initial rotation of the surface around the y back to front axis z rotation deg Specifies the initial rotation of the surface around the z bottom to up axis 7 8 2 The patch selection dialog The surface patches are loaded with
346. rfer MRI viewer program tkmedit to work in conjunction with mne_analyze After a few moments both tkmedit with the current subject s T1 MRI data shown and the MRI viewer control window shown in Figure 7 30 appear Note that the tkmedit user interface is initially hidden The surfaces of a subject must be loaded before starting the MRI viewer The MRI viewer control window contains the following items Show MRI viewer user interface If this item is checked the tkmedit user interface window will be show Track surface location in MRI With this item checked the cursor in the MRI data window follows the current clicked location in surface display or viewer Note that for the viewer window the surface location will inquired from the surface closest to the viewer The MEG helmet surface will not be considered For example if you click at an EEG electrode location with the scalp surface displayed the location of that electrode on the MSH MNE Interactive analysis B MSH MNE scalp will be shown The cortical surface locations are inquired from the white matter surface Show dipole locations in MRI If this option is selected whenever a dipole is displayed in the sur face view using the dipole list dialog discussed in Section 7 15 3 the cursor will also move to the same location in the MRI data window Show digitizer data in MRI If digitizer data are loaded this option shows the locations with green diamonds in the MRI data In
347. riangles However this number of triangles results in a long computation time even in a workstation with generous amounts of memory Therefore the triangulations have to be decimated Speci fying ico 4 yields 5120 triangles per surface while ico 3 results in 1280 triangles The recommended choice is ico 4 MSH MNE The Cookbook a MSH MNE homog Use a single compartment model brain only instead a three layer one scalp skull and brain Only the inner skull tri trian gulation is required This model is usually sufficient for MEG but invalid for EEG If you are employing MEG data only this option is recommended because of faster computation times If this flag 1s specified the options brainc skullc and scalpc are irrelevant brainc lt conductivity S m gt Defines the brain compartment conductivity The default value is 0 3 S m Skulle lt conductivity S m gt Defines the skull compartment conductivity The default value is 0 006 S m corresponding to a conductivity ratio 1 50 between the brain and skull compartments scalpc lt conductivity S m gt Defines the brain compartment conductivity The default value is 0 3 S m innershift lt value mm gt Shift the inner skull surface outwards along the vertex normal direc tions by this amount outershift lt value mm gt Shift the outer skull surface outwards along the vertex normal direc tions by this amount scalpshift lt value mm gt Sh
348. rk locations using the Landmarks dialog 1f necessary 8 Save the aligned file to the file suggested in the dialog coming up from File Save B 3 Mature software B 3 1 This Section contains documentation for software components which are still available in the MNE software but have been replaced by new pro grams mne_compute_mne This chapter contains information about the options accepted by the pro gram mne_compute_mne which is gradually becoming obsolete All of its functions will be eventually included to mne_make_movie see Section 6 5 At this time mne_compute_mne is still needed to produce time collapsed w files unless you are willing to write a Matlab script of your own for this purpose mne_compute_mne accepts the following command line options version Show the program version and compilation date help List the command line options Inv lt name gt Load the inverse operator decomposition from here meas lt name gt Load the MEG or EEG data from this file set lt number gt The data set condition number to load The list of data sets can be seen e g in mne_analyze mne_browse_raw and xplotter bmin lt time ms gt Specifies the starting time of the baseline In order to activate base line correction both bmin and bmax options must be present bmax lt time ms gt Specifies the finishing time of the baseline 327 B Setup at the Martinos Center 328 nave lt va
349. rm Message area time point selection text field an ECD fit button a text field for selecting a vertex on the surface and a message text label Display area for the current estimates Controls for the current estimate display 8 Topographical display of data mM BWN DN 7 4 The menus 7 4 1 The File menu The File shown in Figure 7 2 contains the following items MSH MNE 147 A Interactive analysis 148 Open raw switch to data set Change working directory Load Surface Load morphing surface Load surface patch Load morphing surface patch Load digitizer data View continuous HP data Manage overlays save bad channel selection Quit AIEG Figure 7 2 The File menu Open Load a new data set and an inverse operator For details see Section 7 5 Open raw Load epoch data from a raw data file For details see Section 7 6 Switch to data set If multiple data sets or epochs from a raw data file are loaded this menu item brings up a list to switch between the data sets or epochs Change working directory Change the working directory of this program This will usually be the directory where your MEG EEG data and inverse operator are located Load surface Load surface reconstructions for the subject whose data you are analyzing see Section 7 8 Load morphing surface Load surface reconstructions of another subject for morphing see Section 7 9
350. rmation set to facilitate interpretation by postprocessing software as follows channel name Will be set to J xyz lt number gt where the source component is indicated by the coordinat axis name and number is the vertex num ber starting from zero in the complete triangulation of the hemi sphere in question logical channel number Will be set to is the vertex number starting from zero in the com plete triangulation of the hemisphere in question sensor location The location of the vertex in head coordinates or in MRI coordi nates determined by the mricoord flag sensor orientation The x direction unit vector will point to the direction of the current Other unit vectors are set to zero Again the coordinate system in which the orientation is expressed depends on the mricoord flag The align z flag tries to align the signs of the signals at different vertices of the label For this purpose the surface normals within the label are collected into a n eX 3 matrix The preferred orientation will be taken as the first right singular vector of this matrix corresponding to its largest singular value If the dot product of the surface normal of a vertex is negative the sign of the estimates at this vertex are inverted The inver sion is reflected in the current direction vector listed in the channel infor mation see above Tip The raw data files output by mne_compute_raw_inverse can be con verted to mat files with mne_ra
351. rocesss_raw command line makeproj Estimate the noise subspace from the data and create a new signal Space projection operator instead of using one attached to the data file or those specified with the proj option The following eight options define the parameters of the noise subspace estimation More information on the signal space projection can be found in Section 4 16 projevent lt no gt Specifies the events which identify the time points of interest for projector calculation When this option is present projtmin and projtmax are relative to the time point of the event rather than the whole raw data file MSH MNE Processing raw data 4 MSH MNE projtmin lt time s gt Specify the beginning time for the calculation of the covariance matrix which serves as the basis for the new SSP operator This option is required with projevent and defaults to the begin ning of the raw data file otherwise This option is effective only if makeproj or Saveprojtag options are present projtmax lt time s gt Specify the ending time for the calculation of the covariance matrix which serves as the basis for the new SSP operator This option 1s required with projevent and defaults to the end of the raw data file otherwise This option is effective only if makeprojJ or Saveprojtag options are present projngrad lt number gt Number of SSP components to include for planar gradiometers default 5 This value is
352. rporate the MRI con straint The software to create a source covariance matrix file from MSH MNE The current estimates Lo MSH MNE fMRI data will be provided in a future release of this software pack age depth Employ depth weighting For details see Section 6 2 10 weightexp lt value gt This parameter determines the steepness of the depth weighting function default 0 8 For details see Section 6 2 10 weightlimit lt value gt Maximum relative strength of the depth weighting default 10 For details see Section 6 2 10 fmri lt name gt With help of this w file an a priori weighting can be applied to the source covariance matrix The source of the weighting is usually fMRI but may be also some other data provided that the weighting can be expressed as a scalar value on the cortical surface stored in a w file It is recommended that this w file is appropriately smoothed see Section 8 3 in mne_analyze tksurfer or with mne_smooth_w to contain nonzero values at all vertices of the triangular tessellation of the cortical surface The name of the file given is used as a stem of the w files The actual files should be called lt name gt lh pri and lt name gt rh pri for the left and right hemsphere weight files respectively The application of the weighting is discussed in Section 6 2 11 fmrithresh lt value gt This option is mandatory and has an effect only if a weighting func tion has been specif
353. rpose 31 al The Cookbook 32 3 11 Another useful tool for the coordinate system alignment is MRIlab the Neuromag MEG MRI integration tool Section 3 3 1 of the MRIlab User s Guide Neuromag P N NM20419A A contains a detailed descrip tion of this task Employ the images in the set mri T1l neuromag sets COR fif for the alignment Check the alignment carefully using the digitization data included in the measurement file as described in Sec tion 5 3 1 of the above manual Save the aligned description file in the same directory as the original description file without the alignment infor mation but under a different name Warning This step is extremely important If the alignment of the coor dinate frames is inaccurate all subsequent processing steps suffer from the error Therefore this step should be performed by the person in charge of the study or by a trained technician Written or photographic documenta tion of the alignment points employed during the MEG EEFG acquisition can also be helpful Computing the forward solution After the MRI MEG EEG alignment has been set the forward solution i e the magnetic fields and electric potentials at the measurement sensors and electrodes due to dipole sources located on the cortex can be calcu lated with help of the convenience script mne_do_forward_solution This utility accepts the following options subject lt subject gt Defines the name of the subject This can be als
354. rred by doing a middle mouse button drag and drop from the label showing the current time underneath the display area itself MSH MNE Interactive analysis A Note The cliplab drag and drop functionality requires that you have the proprietary Elekta Neuromag analysis software installed mne_analyze is compatible with cliplab versions 1 2 13 and later MSH MNE 201 A Interactive analysis 202 MSH MNE CHAPTER 8 Morphing and averaging 8 1 Overview The spherical morphing of the surfaces accomplished by FreeSurfer can be employed to bring data from different subjects into a common anatom ical frame This chapter describes utilities which make use of the spherical morphing procedure mne_morph_labels morphs label files between sub jects allowing the definition of labels in a one brain and transforming them to anatomically analogous labels in another mne_average_estimates offers the capability to compute averages of data computed with the MNE software across subjects 8 2 The morphing maps MSH MNE The MNE software accomplishes morphing with help of morphing maps which can be either computed on demand or precomputed using mne_make_morph_maps see Section 8 4 The morphing is performed with help of the registered spherical surfaces lh sphere reg and rh sphere reg which must be produced in FreeSurfer A morphing map is a linear mapping from cortical surface values in subject A x to those in another subject B x PB
355. rs are computed Note Because all morphing map files contain maps in both directions the choice of from and to options only affect the naming of the mor phing map files to be produced mne_make_morph_maps creates direc tory SSUBJECTS DIR morph maps if necessary 8 5 Morphing label data In some instances it is desirable to use anatomically equivalent labels for all subjects in a study This can be accomplished by creating a set of labels in one subject and morphing them to another subjects anatomy using the spherical morphing procedure mne_morph_labels was created to facili tate this task It has the following command line options version Show the program version and compilation date help List the command line options from lt subject gt Name of the subject for which the labels were originally defined to lt subject gt Name of the subject for which the morphed labels should be cre ated labeldir lt directory gt A directory containing the labels to morph prefix lt prefix gt Adds lt prefix gt in the beginning of the output label names A dash will be inserted between lt prefix gt and the rest of the name smooth lt number gt Apply smoothing with the indicated number of iteration steps see Section 8 3 to the labels before morphing them This is advisable because otherwise the resulting labels may have little holes in them since the morphing map is not a bijection By default two smooth
356. s determined so that the strength of each of the dipoles in a label will be 50 nAm WN Let us denote the sums of the magnetic fields and electric potentials pro duced by the dipoles normal to the cortical mantle at label k by x The simulated signals are then N S x X a nC k 1 where M is the number of sources 11 13 5 Source waveform expressions The timecourse option provides flexible possibilities to define the source waveforms in a functional form The source waveform expression files consist of lines of the form lt variable gt lt arithmetic expression gt Each file may contain multiple lines At the end of the evaluation only the values in the variable y q are significant see Table 11 3 They assume MSH MNE 295 1 Miscellaneous utilities 296 the role of q t to compute the simulated signals as described in Section 11 13 4 above All expressions are case insensitive The variables are vectors with the length equal to the number of samples in the responses determined by the tmin tmax and sfreq options The available variables are listed in Table 11 3 ae ae a snmymiry a b c d help variables initialized to Zeros Table 11 3 Available variable names in source waveform expressions The arithmetic expressions can use usual arithmetic operations as well as mathematical functions listed in Table 11 4 The arguments can be vectors or scalar numbers In addition standard re
357. s instead of names containing the vertex numbers out lt name gt Required with labeldir This is the output file for the data extra lt name gt By default the output includes the current estimate signals and the digital trigger channel see digtrig option below With the extra option a custom set of additional channels can be included The extra channel text file should contain the names of these chan nels one channel name on each line With this option present the digital trigger channel is not included unless specified in the extra channel file noextra No additional channels will be included with this option present digtrig lt name gt Name of the composite digital trigger channel The default value 1s STI 014 Underscores in the channel name will be replaced by spaces Split lt size MB gt Specifies the maximum size of the raw data files saved By default the output is split into files which are just below 2 GB so that the fif file maximum size is not exceed Tip The digital trigger channel can also be set with the MNE_TRIGGER CH NAME environment variable Underscores in the variable value will not be replaced with spaces by mne_compute_raw_inverse Using the digtrig option supersedes the MNE_TRIGGER CH NAME environment variable 143 6 The current estimates 144 6 6 2 Implementation details The fif files output from mne_compute_raw_inverse have various fields of the channel info
358. s run and morphing is requested the software first looks for already existing morphing maps there Also 1f mne_analyze or mne_make_movie have to recompute any morphing maps they will be saved to SSUBJECTS DIR morph maps if this directory exists The names of the files in SSUBJECTS DIR morph maps are of the form lt A gt lt B gt morph fif where lt A gt and lt B gt are names of subjects These files contain the eS for both hemispheres and in both directions i e both M4 and M as defined above Thus the files lt A gt lt B gt morph fif or lt B gt lt A gt morph fif are functionally equivalent The name of the file produced by mne_analyze or mne_make_movie depends on the role of lt A gt and lt B gt in the analysis If you choose to compute the morphing maps in batch in advance use mne_make_morph_maps which accepts the following command line options version Show the program version and compilation date help List the command line options redo Recompute the morphing maps even if they already exist from lt subject gt Compute morphing maps from this subject to lt subject gt Compute morphing maps to this subject 205 8 Morphing and averaging 206 all Do all combinations If this is used without either from or to options morphing maps for all possible combinations are com puted If from or to is present only maps between the speci fied subject and all othe
359. s can be moved to one of the Elekta Neuromag report com poser cliplab view areas with the middle mouse button Note When selecting bad channels switch the signal space projection off from the projection dialog Otherwise bad channels may not be easily rec ognizable Note The cliplab drag and drop functionality requires that you have the proprietary Elekta Neuromag analysis software installed mne_browse_raw is compatible with cliplab versions 1 2 13 and later Browsing data If the strip chart display has the input focus click on it 1f you are unsure the keyboard and mouse can be used to browse the data as follows Up and down arrow keys Activate the previous or next selection in the selection list Left and right arrow keys If a single time point is selected green line move the time point forward and backward by I ms If the shift key is down the time point is moved by 10ms If the control key is down with or with out shift the time point is moved by 100ms If mne_browse_raw is controlling mne_analyze see Section 4 18 the mne_analyze dis plays will be updated accordingly If the picked time point falls out side the currently displayed section of data the display will be automatically scrolled backwards or forwards as needed Rotate the mouse wheel or rotate the trackball up down Activate the previous or next selection in the selection list Rotate the trackball left right or rotate the wheel with shift down
360. s read from the data file Save only those event which are not designated as user defined These are typically the events corresponding to changes in the digi tal trigger channel Another possible source for these events is an event file manually loaded without the Add as user events option Save events created here Save the user defined events Save all trigger line transitions By default only those events which are associate with a transition from zero to non zero value are saved These include the user defined events and leading edges of pulses on the trigger line When this option is present all events included with the two above options are saved regardless the type of transition indicated zero to non zero non zero to another non zero value and non zero value to Zero MSH MNE Processing raw data 4 MSH MNE 4 10 4 4 10 5 Tip If you have a text format event file whose content you want to include as user defined events and create the automatic annotation file described in Section 4 10 1 proceed as follows 1 Load the event file with the option Add as user events set 2 Open another data file or quit mne_browse_raw 3 Optionally remove unnecessary events using the event list dialog The directory in which the raw data file resides now contains an annota tion file which will be automatically loaded each time the data file is opened A text format event file suitable for this purpose can be created manually extrac
361. s set only MEG channels are included fixed Use fixed source orientations normal to the cortical mantle By default the source orientations are not constrained If fixed is specified the lLoose flag is ignored loose lt amount gt Use a loose orientation constraint This means that the source covariance matrix entries corresponding to the current component normal to the cortex are set equal to one and the transverse compo nents are set to lt amount gt Recommended value of amount is 0 1 0 6 MSH MNE The Cookbook al depth Employ depth weighting with the standard settings For details see Sections 6 2 10 and 6 4 bad lt name gt Specifies a text file to designate bad channels listed one channel name like MEG 1933 on each line of the file Be sure to include both noisy and flat non functioning channels in the list If bad channels were designated using mne_mark_bad_channels in the measurement file which was specified with the meas option when the forward solution was computed the bad channel informa tion will be automatically included Also any bad channel informa tion in the noise covariance matrix file will be included Senscov lt name gt Name of the noise covariance matrix file computed with one of the methods described in Section 3 12 By default the script looks for a file whose name is derived from the forward solution file by replac ing its ending lt anything gt fwd f1if by
362. s sorted by time e User defined events are automatically kept in a fif format annotation file see Section 4 10 e Added the delay parameter to the averaging and covariance matrix esti mation description files see Sections 4 13 3 and 4 14 3 Detailed information on these changes can be found in Chapter 4 D 3 3 5 mne_compute_raw_inverse The digtrig extra noextra split labeldir and out options were added see Section 6 6 D 3 3 6 mne_convert_surface The functionality of mne_convert_dfs was integrated into mne_convert_surface Text output as a triangle file and and file file con taining the list of vertex points was added The Matlab output option was removed Consequently mne_convert_dfs mne_surface2mat and mne_list_surface_nodes were deleted from the distribution D 3 3 7 mne_dump_ triggers This obsolete utility was deleted from the distribution 343 D Release notes 344 D 3 3 8 mne_epochs2mat The name of the digital trigger channel can be specified with the MNE_TRIGGER_CH_NAME environment variable see Section 9 14 Added the digtrigmask option D 3 3 9 mne_forward_solution Added code to compute the derivatives of with respect to the dipole posi tion coordinates see Section 5 9 D 3 3 10 mne_list_ bem The surfno option is replaced with the id option see Section 9 6 D 3 3 11 mne_make_cor_set Include data from mgh mgz files to the output automatically Include the Talairach transf
363. s the following command line options version Show the program version and compilation date help List the command line options MSH MNE The forward solution a MSH MNE fwd lt name gt lt weight gt Specifies a forward solution to include If no weight is specified 1 0 is asssumed In the averaging process the weights are divided by their sum For example if two forward solutions are averaged and their spefied weights are 2 and 3 the average is formed with a weight of 2 5 for the first solution and 3 5 for the second one out lt name gt Specifies the output file which will contain the averaged forward solution 119 5 The forward solution 120 MSH MNE CHAPTER 6 MSH MNE 6 1 The current estimates Overview This Chapter describes the computation of the minimum norm estimates This is accomplished with two programs mne_inverse_operator and mne_make_movie The chapter starts with a mathematical description of the method followed by description of the two software modules The interactive program for inspecting data and inverse solutions mne_analyze is covered in Chapter 7 6 2 Minimum norm estimates 6 2 1 This section describes the mathematical details of the calculation of mini mum norm estimates In Bayesian sense the ensuing current distribution is the maximum a posteriori MAP estimate under the following assump tions 1 The viable locations of the currents are constrained t
364. schl M I Sereno and A M Dale Cortical surface based analysis II Inflation flattening and a surface based coordinate system Neuroim age vol 9 pp 195 207 1999 B Fischl M I Sereno R B Tootell and A M Dale High resolution intersubject averaging and a coordinate system for the cortical surface Hum Brain Mapp vol 8 pp 272 84 1999 13 3 Forward modeling M S H m l inen and J Sarvas Realistic conductivity geometry model of the human head for interpretation of neuromagnetic data IEEE Trans Biomed Eng vol BME 36 pp 165 171 1989 MSH MNE 315 13 Useful reading 316 B Fischl D H Salat A J van der Kouwe N Makris F Segonne B T Quinn and A M Dale Sequence independent segmentation of magnetic resonance images Neuroimage vol 23 Suppl 1 pp S69 84 2004 F Segonne A M Dale E Busa M Glessner D Salat H K Hahn and B Fischl A hybrid approach to the skull stripping problem in MRI Neuroimage vol 22 pp 1060 75 Jul 2004 J Jovicich S Czanner D Greve E Haley A van der Kouwe R Gollub D Kennedy F Schmitt G Brown J Macfall B Fischl and A Dale Reliability in multi site structural MRI studies effects of gradient non linearity correction on phantom and human data Neuroimage vol 30 pp 436 43 2006 J C Mosher R M Leahy and P S Lewis EEG and MEG forward solutions for inverse methods IEEE Trans Biomed Eng vol 46 p
365. se rights that Licensor has been authorized by a third party to grant to you and accordingly you are solely responsible for obtaining any permissions from third parties which are necessary to use and copy the Software Compliance with Law You must comply with all applicable govern mental laws regulations and orders including without limitation those relating to export and import control in exercising your rights under this Agreement Termination You may terminate this Agreement at any time by destroying all copies of the Software Licensor may terminate this Agreement at any time by providing notice to you of such termination Any use or copying of the Software by you which is inconsistent with the terms and conditions of this Agreement shall automatically render this Agreement null and void and terminate the license granted hereun der Upon any termination of this Agreement you must stop using the Software and return or destroy all copies of the Software including any portion thereof DISCLAIMERS YOU ACKNOWLEDGE THAT THE SOFTWARE HAS BEEN DESIGNED FOR RESEARCH PURPOSES ONLY AND HAS NOT BEEN REVIEWED OR APPROVED BY THE FOOD AND DRUG ADMINISTRATION OR BY ANY OTHER AGENCY AND YOU FURTHER ACKNOWLEDGE THAT CLINICAL APPLI CATIONS ARE NEITHER RECOMMENDED NOR ADVISED The Software is provided AS IS is experimental may contain errors and is subject to further development and revision Licensor does not guar antee the accurac
366. set the environment variable SAMPLE to lt yourdir gt The following tutorial examples assume you have done this 5 Set up the FreeSurfer environment using the commands specific to your site The FreeSurfer license is needed for the source space cre ation covered in Section 12 5 2 Note From this point on directories and files under your personal copy of the sample data set under lt yourdir gt will be referred to by relative pathnames For example the file lt yourdir gt MEG sample aud vis ave will be simply called MEG sample audvis ave Note You can also proceed without FreeSurfer installed if you choose to use source space creation using the recursively subdivided octahedron or icosahedron method For more information see the Note in Section 12 5 2 12 4 Contents of the data set The sample data set contains two main directories MEG sample the MEG EEG data and subjects samp1le the MRI reconstructions An overview of the data provided is given in Tables 12 2 and 12 3 In addition to subject sample the MRI surface reconstructions from another subject morph are provided to demonstrate the morphing capabilities of the MNE software O mw Contents sample audvis_raw fif The raw MEG EEG data A template script for off line averaging auvis Cov A template script for the computation of a noise covariance matrix Table 12 2 Contents of the MEG sample directory Directory for the forward modelling data bem watersh
367. sion Show the program version and compilation date help List the command line options header lt name gt The name of the BrainVision header file The extension of this file is vhdr The header file typically refers to a marker file vmrk which is automatically processed and a digital trigger channel STI 014 is formed from the marker information The vmrk file is ignored if the eximia option is present dig lt name gt The name of the fif file containing the digitization data orignames Use the original EEG channel labels If this option is absent the EEG channels will be automatically renamed to EEG 001 EEG 002 etc eximia Interpret this as an eXimia data file The first three channels will be thresholded and interpreted as trigger channels The composite digi tal trigger channel will be composed in the same way as in the mne_kit2fiff utility see Section 9 2 7 above In addition the fourth channel will be assigned as an EOG channel This option is nor mally used by the mne_eximia2scipt see Section 9 2 11 225 9 Data conversion 226 9 2 11 Split lt size MB gt Split the output data into several files which are no more than lt size gt MB By default the output is split into files which are just below 2 GB so that the fif file maximum size is not exceeded out lt filename gt Specifies the name of the output fif format data file If lt filename gt ends with fif or raw fif these endings
368. sources selected from the complete source spaces Each row contains the number of the source in the complete source space starting with 0 and the source space number 1 or 2 These numbers refer to the order the two hemispheres where listed when mne_make_source_space was invoked mne_setup_source_space lists the left hemi sphere first source_selection Name of the coordinate frame employed in the forward calculations Possible values are head coord_frame string and mri mri_head_trans 4x4 The coordinate frame transformation from mri the MEG head coordinates meg_head_trans 4x4 The coordinate frame transformation from the MEG device coordinates to the MEG head source_COV nsource The elements of the diagonal source covariance matrix Table 9 3 The fields of Matlab structures coordinates 242 MSH MNE Data conversion a eset sing nchan The singular values of A C GRS UAV with R selected so that trace AA trace I 1 as discussed in Section 6 2 3 eigen_fields nchan x nchan The rows of this matrix are the left singular vectors of A 1 e the columns of U see above eigen_leads nchan x nsource The rows of this matrix are the right singular vectors of A 1 e the columns of V see above noise_eigenval noise_eigenvec nchan In terms of Section 6 2 3 eigenvalues of Co 1 e not scaled with number of averages nchan Eigenvectors of the noise covariance matr
369. space information from a fif file Table 10 9 High level routines for reading MNE data files Write a covariance matrix to an open file mne_write_cov_file Write a complete file containing just a covariance matrix mne_write_events Write a fif format event file compatible with mne_browse_raw and mne_process_raw mne_write_inverse_sol_stc Write stc files containing an inverse solution or other dynamic data on the cortical surface mne_write_inverse_sol_w Write w files containing an inverse solution or other Static data on the cortical surface Table 10 10 High level routines for writing MNE data files Funcion Purpose mne_label_time_courses Extract time courses corresponding to a label from an stc file Table 10 11 Routines related to stc w and label files a e mne_read_curvature Read a curvature file Table 10 12 Routines for reading FreeSurfer surfaces 258 MSH MNE The Matlab toolbox 10 mne_read_surface Read one surface return the vertex locations and trian gulation info mne_read_surfaces Read surfaces corresponding to one or both hemi spheres Optionally read curvature information and add derived surface data mne_reduce_surface Reduce the number of triangles on a surface using the reducepatch Matlab function Write a FreeSurfer surface file Table 10 12 Routines for reading FreeSurfer surfaces e Popes mne_block_diag Create a sparse block diagonal matrix out of a vector mne_combine_
370. spectively The data before and after compensation denoted here by x q and x respectively are related by Xp McgyX oy gt where the composite compensation matrix 1s 1 Cy 0 My 0 I 0 0 0 I In the above C is an by n compensation data matrix corresponding to compensation grade k It is easy to see that 215 9 Data conversion 216 9 2 5 L Cik 0 Mi 0 L 0 0 0 I To convert from compensation grade k to p one can simply multiply the inverse of one compensate compensation matrix by another and apply the product to the data E Xo MoMo This operation is performed by mne_compensate_data which has the fol lowing command line options version Show the program version and compilation date help List the command line options In lt name gt Specifies the input data file out lt name gt Specifies the output data file grad lt number gt Specifies the desired compensation grade in the output file The value can be 1 2 3 or 101 The values starting from 101 will be used for 4D Magnes compensation matrices Note Only average data is included in the output Evoked response data files produced with mne_browse_raw or mne_process_raw may include standard errors of mean which can not be re compensated using the above method and are thus omitted Tip Raw data cannot be compensated using mne_compensate_data For this purpose load the data to mne_browse_raw or mne_
371. ssing this defines the beginning point of the raw data range to be included tmax lt time s gt End time point of the epoch If the event parameter is zero or missing this defines the end point of the raw data range to be included bmin lt time s gt It is possible to remove a baseline from the epochs before they are included in the covariance matrix estimation This parameter defines the starting point of the baseline This feature can be employed to avoid overestimation of noise in the presence of low frequency drifts Setting of bmin and bmax is always recommended for epoch based covariance matrix estimation basemin lt time s gt Synonym for bmin bmax lt time s gt End time point of the baseline see above basemax lt time s gt Synonym for bmax 4 15 Managing averages This selection pops up a dialog which allows the management of com puted averages The controls in the dialog shown in Figure 4 15 allow the following Select which categories conditions are displayed in the average view Select the colors of the traces Viewing the log information accumulated in the averaging process Saving of averaged data Setting the active vectors for signal space projection if the data were loaded from a file 6 Setting the current software gradient compensation for data loaded from a file MB WN MSH MNE Processing raw data 4 MSH MNE 4 16 4 16 1 Available averages sample
372. st of all currently loaded labels for ROI analysis Discard all labels Discard all labels loaded so far The label list window will be hid den Clear marked vertices Clear the label outline or a label created interactively 7 4 5 The Dipoles menu The contents of the dipoles menu is shown in Figure 7 6 Dipoles setup fitting show dipole list Manage channel selections Figure 7 6 The dipole fitting menu Setup fitting Define the dipole fitting parameters see Section 7 15 1 Show dipole list Show the list of imported and fitted dipoles see Section 7 15 3 Manage channel selections Manage the selections of channels used in dipole fitting see Section 7 15 4 7 4 6 The Help menu The contents of the Help menu is shown in Figure 7 7 Help _ On version On license On GLA Why the beep Figure 7 7 The Help menu MSH MNE 151 Ea Interactive analysis On version Displays the version and compilation date of the program On license Displays the license information On GLX Displays information about the OpenGL rendering context If you experience poor graphics performance check that the window that pops up from here says that you have a Direct rendering context If not either your graphics card or driver software needs an update Why the beep In some simple error situations mne_analyze does not popup an error dialog but refuses the action and rings the bell
373. standard sphere center x y 0 and z 40 mm instead prad lt value gt Specifies a non standard projection radius R see above 285 1 Miscellaneous utilities 286 width lt value gt Specifies the width of the viewports Default value 5 height lt value gt Specifies the height of the viewports Default value 4 11 7 Adding topology information to a source space 11 7 1 Purpose The utility mne_add_patch_info uses the surface topology information to add data about cortical patches corresponding to each source space point to a source space file A new copy of the source space is created with the patch information included Note Depending on the speed of your computer mne_add_patch_info takes 5 30 minutes to run 11 7 2 Command line options mne_add_patch_info accepts the following command line options version Show the program version and compilation date help List the command line options Ssrcp lt name gt The input source space file The source space files usually end with src fif srcp lt name gt The output source space file which will contain the patch informa tion If the file exists it will overwritten without asking for permis sion A recommended naming convention is to add the letter p after the source spacing included in the file name For example if the input file is mh 7 src fif a recommended output file name is mh 7p srce fif w lt name gt Name of a w file
374. starting time of the baseline In order to activate base line correction both bmin and bmax options must be present bmax lt time ms gt Specifies the finishing time of the baseline baselines lt file_name gt Specifies a file which contains the baseline settings Each line of the file should contain a name of a channel followed by the baseline value separated from the channel name by a colon The baseline values must be specified in basic units 1 e Teslas meter for gradi ometers Teslas for magnetometers and Volts for EEG channels If some channels are missing from the baseline file warning messages are issued for these channels the bmin and bmax settings will be used 6 5 4 Options controlling the estimates nave lt value gt Specifies the effective number of averaged epochs in the input data Le aS discussed in Section 6 3 If the input data file is one pro duced by mne_browse_raw or mne_process_raw the number of averages is correct in the file However if subtractions or some more complicated combinations of simple averages are produced e g by using the xplotter software the number of averages should be man ually adjusted along the guidelines given in Section 6 3 This is accomplished either by employing this flag or by adjusting the num MSH MNE The current estimates ol MSH MNE ber of averages in the data file with help of the utility mne_change_nave snr lt value gt An estimate fo
375. subject can be used as a surrogate if the MRIs of a subject are not available The MNE software comes with additional files which facilitate the use of the average subject in conjunction with mne_analyze These files are located in the directory MNE_ROOT mne setup mne_analyze fsaver age fsaverage_head fif The approximate head surface triangulation for fsaverage fsaverage_inner_skull bem fif The approximate inner skull surface for fsaverage fsaverage fiducials fif The locations of the fiducial points LPA RPA and nasion in MRI coordinates see Section 7 16 2 fsaverage trans fif Contains a default MEG MRI coordinate transformation suitable for fsaverage For details of using the default transformation see Section 7 5 7 20 Compatibility with cliplab The following graphics displays are compatible with the Elekta Neuro mag report composer cliplab The main surface display area in the main window see Section 7 8 The viewer see Section 7 10 The sample channel display see Section 7 7 2 The topographical data display see Section 7 7 1 The SNR time course display see Section 7 12 2 The source time course display seeSection 7 13 Nm BB WN The graphics can be dragged and dropped from these windows to one of the cliplab view areas using the middle mouse button Because the topo graphical display area has another function bed channel selection tied to the middle mouse button the graphics is transfe
376. t Coordinate adjustments Fiducial xMR I mm YMIR mm ZMIRI mm LAP e2 4 lez s12 Nasion Bs B02 js RAP pss as lists Align using fiducials Direction step mm or deg x mm left right lt Blio imm back front lt P fo zimm down up Y Alfo ICP align if steps W Try to keep nasion in place Current coordinate transformation head WRI surface RAS 0 997334 0 065336 0 025611 1 82 mm 0 072617 0 906462 0 411575 297 mm 0 004658 0 412343 0 911016 51 568 mm O O00000 O 000000 0 000000 1 00 mnt save default save MERI set nave Load Figure 7 28 The coordinate frame alignment dialog The coordinate frame alignment dialog contains the following sections MSH MNE 193 A Interactive analysis 194 1 Buttons for picking the fiducial points from the scalp surface and one for setting an initial alignment using these points When one of the fiducials is selected the viewer display automatically rotates to a suit able orientation to make the corresponding fiducial accessible 2 Controls for fine tuning the alignment These include movements along the three orthogonal coordinate axes and rotations around them The buttons marked L and R indicate rotations in counterclockwise and clockwise directions respectively The amount of movement mm or rotation degrees is given in the text fields next to the adjustment but tons 3 Access to an automatic alignment procedure which employs t
377. t End the output files with the specified tag By default the output files will end with mne amp or Spm amp depending on whether MNE or one of the noise normalized estimates dSPM or SLORETA was selected labeloutdir lt directory gt Specifies the directory where the output files will be located By default they will be in the current working directory labelcomments Include comments in the output files The comment lines begin with the percent sign to make the files compatible with Matlab scaleby lt factor gt By default the current values output to the files will be in the actual physical units A m This option allows scaling of the current val ues to other units mne_analyze typically uses 1e10 to bring the numbers to a human friendly scale Using stc file input The stcin option allows input of stc files This feature has several uses 1 QuickTime movies can be produced from existing stc files without having to resort to EasyMeg 2 Graphics snapshot can be produced from existing stc files 3 Existing stc files can be temporally resampled with help of the tmin tmax tstep and integ options MSH MNE The current estimates Lo 4 Existing stc files can be morphed to another cortical surface by specify ing the morph option 5 Timecourses can be inquired and stored into text files with help of the label options see above 6 6 Computing inverse from raw and evoked data 6 6 1
378. t is usually sufficient to run mne_setup_mri without any options Tip If the name specified with the mri option contains a slash the MRI data are accessed from the directory specified and the SUBJECT and SUBJECTS DIR environment variables as well as the subject option are ignored 3 5 Setting up the source space This stage consists of the following 1 Creating a suitable decimated dipole grid on the white matter surface 2 Creating the source space file in fif format 3 Creating ascii versions of the source space file for viewing with MRIIab All of the above is accomplished with the convenience script mne_setup_source_space This script assumes that 1 The anatomical MRI processing has been completed as described in Section 3 3 2 The environment variable SUBJECTS_DIR is set correctly The script accepts the following options 21 al The Cookbook subject lt subject gt Defines the name of the subject If the environment variable SUB JECT is set correctly this option is not required morph lt name gt Name of a subject in SUBJECTS_DIR If this option is present the source space will be first constructed for the subject defined by the subject option or the SUBJECT environment variable and then morphed to this subject This option is useful if you want to create a source spaces for several subjects and want to directly compare the data across subjects at the source space vertices without any mor phing
379. ta This initial value can be changed in the inter active version of the program digtrig lt name gt Name of the composite digital trigger channel The default value is STI 014 Underscores in the channel name will be replaced by spaces digtrigmask lt number gt Mask to be applied to the trigger channel values before considering them This option is useful if one wants to set some bits in a don t care state For example some finger response pads keep the trigger lines high if not in use i e a finger is not in place Yet it is conve nient to keep these devices permanently connected to the acquisition system The number can be given in decimal or hexadecimal format beginning with Ox or OX For example the value 255 OxFF means that only the lowest order byte usually trigger lines 8 or bits O 7 will be considered Note Multiple raw data files can be specified for mne_process_raw Note Strictly speaking trigger mask value zero would mean that all trig ger inputs are ignored However for convenience setting the mask to zero or not setting it at all has the same effect as OXFFFFFFFF i e all bits set Tip The digital trigger channel can also be set with the MNE_TRIGGER CH NAME environment variable Underscores in the variable value will not be replaced with spaces by mne_browse_raw or mne_process_raw Using the digtrig option supersedes the MNE_TRIGGER CH NAME environment variable Tip The digital
380. ta file name and lt tag gt fif or lt tag gt log is appended to create the output and log file names respectively For compatibility with other MNE software scripts savecovtag cov is recommended savehere If the saveavetag and Ssavecovtag options are used to generate the file output file names the resulting files will go to the same directory as raw data by default With this option the output files will be generated in the current working directory instead gCOV lt name gt If multiple raw data files are specified as input and covariance matrix estimation is requested the grand average over all data files will be saved to lt name gt The details of the covariance matrix esti mation are given in Section 4 17 Save lt name gt Save a filtered and optionally down sampled version of the data file to lt name gt If multiple raw data files are specified an equal number of save options should be present If lt filename gt ends with fif or raw fif these endings are deleted After these modifi cations raw fif is inserted after the remaining part of the file name If the file is split into multiple parts see split option below the additional parts will be called lt name gt lt num ber gt _raw fif Split lt size MB gt Specifies the maximum size of the raw data files saved with the save option By default the output is split into files which are just below 2 GB so that the fif file maximum size
381. tant The elp and hpts input files may contain textual EEG elec trode labels They will not be copied to the fif format output MSH MNE Data conversion 9 MSH MNE 9 3 1 The command line options of mne_convert_dig_data are version Show the program version and compilation date help List the command line options fif lt name gt Specifies the name of an input fif file hpts lt name gt Specifies the name of an input Apts file elp lt name gt Specifies the name of an input elp file fifout lt name gt Specifies the name of an output fi file hptsout lt name gt Specifies the name of an output Apts file headcoord The fif and hpts input files are assumed to contain data in the MNE head coordinate system see Section 5 3 With this option present the data are transformed to the MNE head coordinate system with help of the fiducial locations in the data Use this option if this is not the case or if you are unsure about the definition of the coordinate system of the fif and hpts input data This option is implied with elp input files The hpts format The hpts format digitzer data file may contain comment lines starting with the pound sign and data lines of the form lt category gt lt identifier gt lt x mm gt lt y mm gt lt z mm gt where lt calegory gt defines the type of points Allowed categories are hpi cardinal fiducial eeg and extra corresponding to head position i
382. tates to facilitate fiducial picking from the head surface mne_ctf2fiff Correct errors in compensation channel information and compensation data output The transformation between the CTF and Neuromag coordi nate frames is now included in the output file mne_make_movie Added the Labelverts option see Section 6 5 8 mne_surf2bem Added the shift option to move surface vertices outwards Fixed some loopholes in topology checks Also added the innershift option to mne_setup_forward_model For more information see Sections 3 7 and 5 6 mne_forward_ solution Added code to compute forward solutions for CTF data with software gra dient compensation on MSH MNE Release notes D D 2 9 D 2 10 D 2 11 D 2 12 D 2 13 MSH MNE mne_inverse_operator The following changes have been made in mne_inverse_operator e Added options to regularize the noise covariance matrix e Added correct handling of the rank deficient covariance matrix result ing from the use of SSS e Additional projections cannot be specified if the noise covariance matrix was computed with projections on e Bad channels can be added only in special circumstances if the noise covariance matrix was computed with projections on mne_compute_raw_inverse This utility is now documented in Section 6 6 The utility mne_make_raw_inverse_operator has been removed from the software Time range settings The tools mne_compute_raw_inverse mne_convert_mn
383. ted from an EDF file using the tal option in mne_edf2fiff discussed in Section 9 2 8 or produced by custom software used during data acquisition Defining annotated events The Windows Show annotator shows a window to add annotated user defined events In this window the buttons in first column mark one or more selected time points with the event number shown in the second col umn with an associated comment specified in the third column Marking also occurs when return is pressed on any of the second and third column text fields When the dialog is brought up for the first time the file SHOME mne mne_browse_raw annot is consulted for the definitions of the second and third column values i e event numbers and comments You can save the current definitions with the Save defs button and reload the annotation definition file with Load defs The annotation definition file may contain comment lines starting with or and data lines which contain an event number and an optional comment separated from the event number by acolon Tip If you want to add a user defined event without an a comment you can use the Picked to item in the tool bar described in Section 4 11 Event files A text format event file contains information about transitions on the digi tal trigger line in a raw data file Any lines beginning with the pound sign are considered as comments The format of the event file data 1s lt sample gt lt time gt
384. tep fT j 500 Reconstruction surface radius mm 60 0 EEG contour step fu OK Apply Cancel Help Figure 7 20 Field mapping preferences dialog 175 Ea Interactive analysis 176 The Field mapping preferences dialog has the following controls arranged in MEG EEG and common sections SVD truncation at Adjusts the smoothing of the field and potential patterns This parameter specifies the eigenvalue truncation point as described in Section 7 11 2 Smaller values correspond to noisier field patterns with less smoothing Use default origin The location of the origin of the spherical head model used in these computations defaults to 0 0 40 mm If this box is unchecked the origin coordinate fields are enabled to enter a custom origin loca tion Usually the default origin is appropriate Downsampling grade This option only applies to EEG potential maps and MEG field maps extrapolated to the head surface and controls the number of virtual electrodes or point magnetometers used in the interpolation Allowed values are 2 162 locations 3 642 locations and 4 2562 locations Usually the default value 3 is appropriate Number of smoothsteps This option controls how much smoothing see Section 8 3 is applied to the interpolated data before computing the contours Usu ally the default value is appropriate Reconstruction surface radius Distance of the spherical reconstruction surface from the sphere model
385. terpolate voxels Toggles trilinear interpolation in the MRI data on and off Max intensity projection Shows a maximum intensity projection of the MRI data This is useful in conjunction with the Show digitizer data in MRI option to evaluate the MEG MRI coordinate alignment Recenter MRI display Brings the cursor to the center of the MRI data Show surface data in MRI This button creates an MRI data set containing the surface data dis played and overlays in with the MRI slices shown in the MRI viewer Show segmentation data in MRI If available the standard automatically generated segmentation vol ume mri aparc aseg is overlaid on the MRI using the standard FreeSurfer color lookup table S FREESURFER_HOME Free SurferColorLUT txt As a result the name of the brain structure or region of corex at the current location of the cursor will be reported if the tkmedit user interface is visible After the segmentation is loaded this button toggles the display of the segmentation on and off Show command input and output Allows sending tcl commands to tkmedit and shows the responses received The tkmedit tclscripting commands are discussed at https surfer nmr mgh harvard edu fswiki TkMeditGuide TkMeditRefer ence TkMeditScripting 199 A Interactive analysis 200 7 19 Working with the average brain The FreeSurfer software includes an average subject fsaverage with a cortical surface reconstruction In some cases the average
386. ters have to be handled separately see mag option below By default MEG gradiometers are included mag Include MEG magnetometers instead of gradiometers w lt name gt Specifies the stem of the output w files To obtain the final output file names lh w and rh w is appended for the left and right hemisphere respectively 289 1 Miscellaneous utilities 290 11 10 3 smooth lt number gt Specifies the number of smooth steps to apply to the resulting w files Default no smoothing map lt number gt Select the type of a sensitivity map to compute At present valid numbers are 1 6 For details see Section 11 10 3 below Available sensitivity maps In the following let Gy Bex Syk 4 denote the three consecutive columns of the gain matrix G corresponding to the fields of three orthogonal dipoles at source space location k Fur ther lets assume that the source coordinate system has been selected so that the z axis points to the cortical normal direction and the xy plane is thus the tangent plane of the cortex at the source space location k Next compute the SVD and let g u A Where A and u are the largest singular value and the corresponding left singular vector of G respectively It is easy to see that g is has the largest power among the signal distributions pro duced by unit dipoles at source space location k Furthermore assume that the colums orthogonal matrix U p UU p
387. tessellation is loaded as needed Depending on the precise location of the fitted dipole the spot indicating the dipole site may easily appear on a dif ferent wall of a fissure than could be expected The fissural walls can be far apart from each other in the inflated view of the cortex even if they are physically separated by just a few millimeters The size of the spots indi cating the dipole locations do not relate to the dipole strengths or their confidence limits in any way 7 15 4 Channel selections As mentioned in Section 7 7 1 the right mouse button in the topographi cal display of channels can be used to restrict the selection of channels taken into account in dipole fitting In addition the channel selections can be manipulated in the channel selection window which pops up from Dipoles Manage channel selections Initially this dialog contains the selections defined in or HOME mne mne_analyze sel or MNE_ROOT share mne mne_analyze mne_analyze sel the personal file taking prece dence over the system wide default The Save button in this dialog save the current set of channel selections to the personal selection file The for mat of this file is identical to the channel selection file in mne_browse_raw When a channel selection file is in effect the variances of the unselected channels are increased by a factor of 900 This means that unselected channels receive virtually no weight in the least squares error function or equ
388. text format input file The format of this file is described in Section 5 6 3 meters The unit of measure for the vertex locations in a text input files is meters instead of the default millimeters This option does not have any effect on the interpretation of the FreeSurfer surface files speci fied with the surf option Swap Swap the ordering or the triangle vertices The standard convention in the MNE software is to have the vertices in text format files ordered so that the vector cross product of the vectors from vertex 1 to 2 and 1 to 3 gives the direction of the outward surface normal This is also called the counterclockwise ordering If your text input file does not comply with this right hand rule use the swap option This option does not have any effect on the interpretation of the FreeSurfer surface files specified with the surf option surf lt name gt Specifies a FreeSurfer format input file dfs lt name gt Specifies the name of a dfs file to be converted The surfaces pro duced by BrainSuite are in the dfs format mghmri lt name gt Specifies a mgh mgz format MRI data file which will be used to define the coordinate transformation to be applied to the data read from a dfs file to bring it to the FreeSurfer MRI coordinates i e the coordinate system of the MRI stack in the file fifmri lt name gt Specifies a fif format MRI destription file which will be used to define the coordinate transformati
389. the FFT to be applied in filtering The number will be rounded up to the next power of two If the size is N the corresponding length of time is N f where f is the sampling frequency of your data The filtering procedure includes overlapping tapers of length N 2 so that the total FFT length will actually be 2N This value cannot be changed after the program has been started highpass lt value Hz gt Highpass filter frequency limit If this is too low with respect to the selected FFT length and the data will not be highpass filtered It is best to experiment with the interactive version to find the lowest applicable filter for your data This value can be adjusted in the interactive version of the program The default is 0 i e no highpass filter apart from that used during the acquisition will be in effect highpassw lt value Hz The width of the transition band of the highpass filter The default is 6 frequency bins where one bin is f 2N This value cannot be adjusted in the interactive version of the program lowpass lt value Hz gt Lowpass filter frequency limit This value can be adjusted in the interactive version of the program The default is 40 Hz 42 MSH MNE Processing raw data 4 MSH MNE 4 2 2 lowpassw lt value Hz gt The width of the transition band of the lowpass filter This value can be adjusted in the interactive version of the program The default 1s 5 Hz filteroff Do not filter the da
390. the augmented location vectors in MRI head and MRI coordinate systems are denoted by Fead hea E OE eed i and respectively FMRI T lt ri YMRI ZMRI i i rMRI TThead Note It is not possible to calculate an EEG forward solution with a sin gle layer BEM 3 12 Setting up the noise covariance matrix The MNE software employs an estimate of the noise covariance matrix to weight the channels correctly in the calculations The noise covariance matrix provides information about field and potential patterns represent ing uninteresting noise sources of either human or environmental origin The noise covariance matrix can be calculated in several ways 1 Employ the individual epochs during off line averaging to calculate the full noise covariance matrix This is the recommended approach for evoked responses 2 Employ empty room data collected without the subject to calculate the full noise covariance matrix This is recommended for analyzing ongoing spontaneous activity 3 Employ a section of continuous raw data collected in the presence of the subject to calculate the full noise covariance matrix This is the rec ommended approach for analyzing epileptic activity The data used for this purpose should be free of technical artifacts and epileptic activity of interest The length of the data segment employed should be at least 20 seconds One can also use a long gt 200 s segment of data with epi leptic spikes present provided that
391. the data There is an option to keep existing projection items Note Whenever EEG channels are present in the data a projection item corresponding to the average EEG reference is automatically added Save projection The Save projection item in the File menu pops up a dialog to save the present projection operator into a file Normally the EEG average refer ence projection is not included If you want to include it mark the nclude EEG average reference option If your MEG projection includes items for both magnetometers and gradiometers and you want to use the projection operator file output from here in the Neuromag Signal processor graph software mark the Enforce compatibility with graph option 51 4 Processing raw data 52 4 4 7 4 4 8 4 4 9 4 4 10 4 4 11 4 4 12 Apply bad channels Applies the current selection of bad channels to the currently open raw file Load events text Reads a text format event file For more information on events see Section 4 10 Load events fif Reads a fif format event file For more information on events see Section 4 10 Save events text Brings up a a dialog to save all or selected types of events into a text file This file can be edited and used in the averaging and covariance matrix estimation as an input file to specify the time points of events see Section 4 10 5 For more information on events see Section 4 10 Save events fif Save the events
392. the derivation file was created The derived channels can be included in channel selections see Section 4 5 5 At present derived channels cannot be displayed in topographical data displays Derived channels are not included in aver ages or noise covariance matrix estimation Note If the file SHOME mne mne browse raw deriv fif exists and contains derivation data it is loaded automatically when mne_browse_raw starts unless the deriv option has been used to specify a nonstandard derivation file see Section 4 2 2 Save derivations Saves the current derivations into a file Load channel selections This choice loads a new set of channel selections The default directory for the selections is HOME mne If this directory does not exist it will be created before bringing up the file selection dialog to load the selec tions Save channel selections This choice brings up a dialog to save the current channel selections This is particularly useful if the standard set of selections has been modified as explained in Section 4 5 5 The default directory for the selections is HOME mne If this directory does not exist it will be created before bringing up the file selection dialog to save the selections Note that all currently existing selections will be saved not just those added to the ones initially loaded 53 4 Processing raw data 4 4 16 Quit Exits the program without questions asked 4 5 The Adjust menu Filter
393. the forward solution as well as appropriate Inclusion of the projections into the covariance matrix limits the possibilities to use the bad and proj options in mne_inverse_operator see Section 6 4 MSH MNE Processing raw data 4 MSH MNE 4 18 Interacting with mne_analyze To facilitate interactive analysis of raw data mne_browse_raw can run mne_analyze as a child process In this mode mne_analyze is remote controlled by mne_browse_raw and will also send replies to mne_browse_raw to keep the two programs synchronized A practical application of this communication is to view field or potential maps and cortically constrained source estimates computed from raw data instantly The subordinate mne_analyze is started and stopped from Start mne_analyze and Quit mne_analyze in the Windows menu respectively The following settings are communicated between the two processes The raw data file If a new raw data file is opened and a subordinate mne_analyze is active the name of the raw data file 1s communicated to mne_analyze and a simplified version of the open dialog appears in mne_analyze allowing selection of an inverse operator or are MEG MRI coordinate transformation If a raw data file is already open in mne_browse_raw when mne_analyze is started the open dialog appears immediately Time point When a new time point is selected in mne_browse_raw the mne_analyze time point selection is updated accordingly Time point select
394. the license information About current data Displays essential information about the currently loaded data set Why the beep In some simple error situations mne_browse_raw does not pop up an error dialog but refuses the action and rings the bell The reason for this can be displayed through this help menu item 68 MSH MNE Processing raw data 4 4 9 The raw data display The main data displays shows a section of the raw data in a strip chart recorder format The names of the channels displayed are shown on the left The selection of channels is controlled from the selection dialog see Section 4 5 5 The length of the data section displayed is controlled from the scales dialog Section 4 5 2 and the filtering from the filter dialog Section 4 5 1 A signal space projection can be applied to the data by loading a projection operator Section 4 4 5 The selection of the projec tion operator items is controlled from the projection dialog described in Section 4 5 7 The control and browsing functions of the main data display are Selection of bad channels If you click on a channel name the corresponding channel is marked bad or reinstated as an acceptable one A channel marked bad is not considered in the artefact rejection procedures in averaging and it 1s omitted from the signal space projection operations Browsing Browsing through the data The section of data displayed can be selected from the scroll bar at the bottom of the
395. the spikes occur infrequently and 35 al The Cookbook 36 that the segment is apparently stationary with respect to background brain activity The new raw data processing tools mne_browse_raw or mne_process_raw include computation of noise covariance matrices both from raw data and from individual epochs For details see Chapter 4 3 13 Calculating the inverse operator decomposition The MNE software doesn t calculate the inverse operator explicitly but rather computes an SVD of a matrix composed of the noise covariance matrix the result of the forward calculation and the source covariance matrix This approach has the benefit that the regularization parameter SNR can be adjusted easily when the final source estimates or dSPMs are computed For mathematical details of this approach please consult Section 6 2 This computation stage is facilitated by the convenience script mne_do_inverse_operator It invokes the program mne_inverse_operator with appropriate options derived from the command line of mne_do_inverse_operator mne_do_inverse_operator assumes the following options fwd lt name of the forward solution file gt This is the forward solution file produced in the computations step described in Section 3 11 meg Employ MEG data in the inverse calculation If neither meg nor eeg is set only MEG channels are included eeg Employ EEG data in the inverse calculation If neither meg nor eeg i
396. ting with the pound sign are comments A coil definition starts with a description line contain ing the following fields lt class gt This is a number indicating class of this coil Possible values are listed in Table 5 4 lt id gt Coil id value This value is listed in the first column of Tables 5 2 and 5 3 lt accuracy gt The coil representation accuracy Possible values and their mean ings are listed in Table 5 5 lt np gt Number of integration points in this representation lt size m gt The size of the coil For circular coils this is the diameter of the coil and for square ones the side length of the square This information is mainly included to facilitate drawing of the coil geometry It should not be employed to infer a coil approximation for the forward calcu lations lt baseline m gt The baseline of a this kind of a coil This will be zero for magne tometer coils This information is mainly included to facilitate drawing of the coil geometry It should not be employed to infer a coil approximation for the forward calculations 111 a The forward solution 112 lt description gt Short description of this kind of a coil If the description contains several words it is enclosed in quotes ao meom a first order axial gradiometer planar gradiometer second order axial gradiometer 1000 an EEG electrode used inter nally in software only Table 5 4 Coil class values E The simplest re
397. tion for each channel The first three values specify the origin of the sensor coordinate system or the location of the elec trode For MEG channels the following nine number specify the x y and z direction unit vectors of the sensor coordinate system For EEG electrodes the first unit vector specifies the location of the reference electrode If the refer ence is not specified this value is all zeroes The remaining unit vectors are irrelevant for EEG electrodes Logical channel numbers as listed in the fi file Table 9 3 The fields of Matlab structures MSH MNE 241 Data conversion wae se ttn ch_units nchan x 2 Units and unit multipliers as listed in the fif file The unit of the data is listed in the first column T 112 T m 201 V 107 At present the second column will be always zero i e no unit multiplier ch_cals nchan x 2 Even if the data comes from the conversion already calibrated the original calibration fac tors are included The first column is the range member of the fif data structures and while the second is the cal member To get calibrated val ues in the units given in ch_units from the raw data the data must be multiplied with the prod uct of range and cal highpass l Highpass filter frequency Hz source_loc nloc x 3 The source locations given in the coordinate frame indicated by the coord_frame member source_ori nsource x 3 The source orientations nsource x 2 Indication of the
398. tlab toolbox to read the forward solution It is then possible to compute e g volumetric beam former solutions in Matlab and output the results into w or stc files The purpose of the mne_volume_data2mri is to produce MRI overlay data compatible with FreeSurfer MRI viewers in the mgh or mgz formats from this type of w or stc files mne_volume_data2mri accepts the following command line options version Show the program version and compilation date help List the command line options src lt filename gt The name of the volumetric source space file created with mne_volume_source_space The source space must have been cre ated with the mri option which adds the appropriate sparse tri linear interpolator matrix to the source space w lt filename gt The name of a w file to convert into an MRI overlay MSH MNE Data conversion 9 Stc lt filename gt The name of the stc file to convert into an MRI overlay If this file has many time frames the output file may be huge Note If both w and stc are specified w takes precedence scale lt number gt Multiply the stc or w by this scaling constant before producing the overlay out lt filename gt Specifies the name of the output MRI overlay file The name must end with either mgh or mgz identifying the uncompressed and compressed FreeSurfer MRI formats respectively 9 5 Listing source space data The utility mne_list_source_space outputs the sourc
399. trigger channel mask can also be set with the MNE_TRIGGER_CH_MASK_ environment variable Using the digtrigmask option supersedes the MNE_TRIGGER_CH_MASK environment variable Interactive mode options These options apply to the interactive mne_browse_raw version only 43 4 Processing raw data 44 4 2 3 allowmaxshield Allow loading of unprocessed Elekta Neuromag data with Max Shield on These kind of data should never be used for source local ization without further processing with Elekta Neuromag software deriv lt name gt Specifies the name of a derivation file This overrides the use of a standard derivation file see Section 4 4 12 sel lt name gt Specifies the channel selection file to be used This overrides the use of the standard channel selection files see Section 4 5 5 Batch mode options These options apply to the batch mode version mne_process_raw only proj lt name gt Specify the name of the file of the file containing a signal space pro jection SSP operator If proj options are present the data file is not consulted for an SSP operator The operator corresponding to average EEG reference is always added if EEG data are present projon Activate the projections loaded One of the options projon or projoff must be present on the mne_processs_raw command line projoff Deactivate the projections loaded One of the options projon or projoff must be present on the mne_p
400. ts 5 5 Creating a volumetric or discrete source space In addition to source spaces confined to a surface the MNE software pro vides some support for three dimensional source spaces bounded by a sur face as well as source spaces comprised of discrete arbitrarily located source points The mne_volume_source_space utility assists in generating such source spaces The command line options are version Show the program version and compilation date help List the command line options sSurf lt name gt Specifies a FreeSurfer surface file containing the surface which will be used as the boundary for the source space 99 a The forward solution bem lt name gt Specifies a BEM file ending in bem fif The inner skull sur face will be used as the boundary for the source space origin lt x mm gt lt y mm gt lt z mm gt If neither of the two surface options described above is present the source space will be spherical with the origin at this location given in MRI RAS coordinates rad lt radius mm gt Specifies the radius of a spherical source space Default value 90 mm grid lt spacing mm gt Specifies the grid spacing in the source space mindist lt distance mm gt Only points which are further than this distance from the bounding surface are included Default value 5 mm exclude lt distance mm gt Exclude points that are closer than this distance to the center of mass of the boun
401. ts and Wip are the weights associated to the integration points This formula essentially presents numerical integration of the magnetic field over the pickup loops of sensor k There are three accuracy levels for the numerical integration expressed above The simple accuracy means the simplest description of the coil This accuracy is not used in the MNE forward calculations The normal or recommended accuracy typically uses two integration points for planar gradiometers one in each half of the pickup coil and four evenly distrib uted integration points for magnetometers This is the default accuracy used by MNE If the accurate option is specified the forward calcu lation typically employs a total of eight integration points for planar gradi ometers and sixteen for magnetometers Detailed information about the integration points is given in the next section MSH MNE The forward solution al 5 8 3 Implemented coil geometries This section describes the coil geometries currently implemented in Neu romag software The coil types fall in two general categories 1 Axial gradiometers and planar gradiometers and 2 Planar gradiometers For axial sensors the z axis of the local coordinate system is parallel to the field component detected i e normal to the coil plane For circular coils the orientation of the x and y axes on the plane normal to the z axis is irrelevant In the square coils employed in the Vectorview system the
402. uced by mne_browse_raw or mne_process_raw the number of averages is correct in the file However 1f subtractions or some more complicated combinations of simple averages are produced e g by using the xplotter software the number of averages should be man ually adjusted along the guidelines given in Section 6 3 This is accomplished either by employing this flag or by adjusting the num ber of averages in the data file with help of the utility mne_change_nave snr lt value gt An estimate for the amplitude SNR The regularization parameter will be set as A 1 SNR The default value is SNR 3 Auto matic selection of the regularization parameter is currently not sup ported Spm Calculate the dSPM instead of the expected current value picknormalcomp The components of the estimates corresponding to directions tan gential with the cortical mantle are zeroed out mricoord Provide source locations and orientations in the MRI coordinate frame instead of the default head coordinate frame label lt name gt Specifies a label file to process For each label file the values of the computed estimates stored in a fif file For more details see Section 6 6 2 The label files are produced by tksurfer or mne_analyze and specify regions of interests ROIs A label file name should end with 1h label for left hemisphere ROIs and with rh label for right hemisphere ones The corresponding output files are tagged with Lh
403. umber and the x y and z coordinates are given The running number is not considered by mne_tri2fiff The nodes must be thus listed in the correct consecutive order X y Z nx ny nz The x y and z coordinates as well as the approximate vertex normal direction cosines are given number x y Z nx ny nz A running number is given in addition to the vertex location and vertex normal Each triangle entry consists of the numbers of the vertices belonging to a triangle The vertex numbering starts from one The triangle list may also contain running numbers on each line describing a triangle 103 a The forward solution 104 5 6 4 Topology checks If the check option is specified the following topology checks are performed 1 The completeness of each surface is confirmed by calculating the total solid angle subtended by all triangles from a point inside the triangula tion The result should be very close to 47 If the result is 47 instead it is conceivable that the ordering of the triangle vertices is incorrect and the swap option should be specified 2 The correct ordering of the surfaces is verified by checking that the sur faces are inside each other as expected This is accomplished by check ing that the sum solid angles subtended by triangles of a surface S at all vertices of another surface S which is supposed to be inside it equals 4r Naturally this check is applied only if the model has more than one surface
404. ume_data2mri Convert volumetric data defined in a source space created with mne_volume_source_space into an MRI overlay see Section 9 4 mne_volume_source_space Make a volumetric source space see Section 5 5 mne_watershed_bem Do the segmentation for BEM using the watershed algo rithm see Section A 1 Table 2 2 Utility programs MSH MNE 15 A Overview 16 2 2 2 3 2 4 File formats The MNE software employs the fif file format whenever possible New tags have been added to incorporate information specific to the calculation of cortically contained source estimates FreeSurfer file formats are also employed when needed to represent cortical surface geometry data as well as spatiotemporal distribution of quantities on the surfaces Of particular interest are the w files which contain static overlay data on the cortical surface and stc files which contain dynamic overlays movies Conventions When command line examples are shown the backslash character indi cates a continuation line It is also valid in the shells In most cases how ever you can easily fit the commands listed in this manual on one line and thus omit the backslashes The order of options is irrelevant Entries to be typed literally are shown like this Italicized text indicates conceptual entries For example lt dir gt indicates a directory name In the description of interactive software modules the notation lt menu gt lt item gt 1s
405. urf subjid lt subject gt Goto the directory SUBJECTS DIR lt subject gt bem Convert the head surface file mne surf2bem surf surf lh smseghead id 4 check fif lt subject gt head dense fif 5 Rename the existing head surface file to lt subject gt head sparse fif 6 Copy lt subject gt head dense fif to lt subject gt head fif 7 Click Reload in the viewer window KRWN Re After this you can switch between the dense and smooth head surface tes sellations by copying either lt subject gt head dense fif or lt sub ject gt head sparse fif to lt subject gt head fif Important While the dense head surface tessellation may help in coordi nate frame alignment it will slow down the operation of the viewer win dow considerably Furthermore it cannot be used in forward modelling due to the huge number of triangles For the BEM the dense tessellation does not provide much benefit because the potential distributions are quite smooth and widespread on the scalp 195 Ea Interactive analysis 196 7 16 2 Using fiducial points identified by other software If you have identified the three fiducial points in software outside mne_analyze it is possible to display this information on the head surface visualization To do this you need to copy the file containing the fiducial location information in MRI surface RAS coordinates to S SUBJECTS_DIR SUBJECT bem SUBJECT fiducials fif There a three supported
406. urface to fif format and saves the result to bem lt subject gt head fif The mne_analyze tool described Chapter 7 looks for this file the visualiza tions involving the scalp surface 319 A Creating the BEM meshes A 2 Using FLASH images 320 A 2 1 This method depends on the availablily of MRI data acquired with a multi echo FLASH sequence at two flip angles 5 and 30 degrees These data can be acquired separately from the MPRAGE data employed in FreeSurfer cortical reconstructions but it is strongly recommended that they are collected at the same time with the MPRAGEs or at least with the same scanner For easy co registration the images should have FOV matrix slice thickness gap and slice orientation as the MPRAGE data For information on suitable pulse sequences see reference B Fischl et al and J Jovicich et al 2006 in Section 13 3 At the Martinos Center use of the 1 5 T Avanto scanner Bay 2 is recommended for best results Creation of the BEM meshes using this method involves the following Steps 1 Organizing the MRI data This is facilitated by the script mne_organize_dicom see Section A 2 1 2 Creating a synthetic 5 degree flip angle FLASH volume register it with the MPRAGE data and run the segmentation and meshing pro gram This step is accomplished by running the script mne_flash_bem see Section A 2 2 3 Inspecting the meshes with tkmedit see Section A 2 3 Note The following sections assume t
407. utational convenience we prefer to take another route which employs the singular value decomposition SVD of the matrix ee ee T A GR UAV where the superscript 1 2 indicates a square root of R For a diagonal matrix one simply takes the square root of R while in the more general case one can use the Cholesky factorization R RoR and thus Rp Ro With the above SVD it is easy to show that y 1 2 T M R V VI U where the elements of the diagonal matrix are 2 Ak 2 l w Maen With w t u C xA the expression for the expected current is i R VEw r Y vewh gt k C where v R v v being the kth column of V It is thus seen that the current estimate is a weighted sum of the modified eigenleads vg MSH MNE The current estimates E MSH MNE 6 2 6 It is easy to see that w t JL To maintain the relation trace GRG trace I 1 when ZL changes we must have R 1 L With this approach A is independent of L and for fixed we see directly that j is independent of L Noise normalization The noise normalized linear estimates introduced by Dale et al require division of the expected current amplitude by its variance Noise normal ization serves three purposes 1 It converts the expected current value into a dimensionless statistical test variable Thus the resulting time and location dependent values are often referred to as dynamic statistical parameter maps dSPM
408. vely This utility renders an inflated brain surface repeatedly rotating it by 5 degrees around the z axis between redraws At each revolution the time spent for the full revolution is reported on the terminal window where mne_opengl_test was started from The program renders the surface until the interrupt key usually control c is pressed on the terminal window mne_opengl_test is located in the bin directory and is thus started as MNE ROOT bin mne opengl test On the fastest graphics cards the time per revolution is well below 1 sec ond If this time longer than 10 seconds either the graphics hardware acceleration is not in effect or you need a faster graphics adapter C 3 Obtain FreeSurfer The MNE software relies on the FreeSurfer software for cortical surface reconstruction and other MRI related tasks Please consult the FreeSurfer home page site at http surfer nmr mgh harvard edu C 4 How to get started After you have installed the software a good place to start is to look at the manual e Source the correct setup script see Section 2 4 and e Say mne view manual Chapters of interest for a novice user include 333 c Installation and configuration e Chapters and 2 contain introduction to the software and setup instruc tions e Chapter 3 is an overview of the necessary steps to compute the corti cally constrained minimum norm solutions e Chapter 12 is a hands on exercise demonstrating analysis of the s
409. w data files in the order given If it is smaller the last description file will be used for the remaining raw data files Saveavetag lt tag gt If this option is present and averaging is evoked with the ave option the outfile and logfile options in the averaging description file are ignored Instead trailing fif or raw fif is removed from the raw data file name and lt tag gt fif or lt tag gt 1log is appended to create the output and log file names respectively gave lt name gt If multiple raw data files are specified as input and averaging is requested the grand average over all data files will be saved to lt name gt COV lt name gt Specify the name of a description file for covariance matrix estima tion For details of the format of this file please see Section 4 14 If multiple raw data files are specified the number of cov options can be smaller or equal to the number of raw data files If it is equal the averaging description file names will be associated with the raw 46 MSH MNE Processing raw data 4 MSH MNE data files in the order given If it is smaller the last description file will be used for the remaining raw data files Savecovtag lt lag gt If this option is present and covariance matrix estimation is evoked with the cov option the outfile and logfile options in the covari ance estimation description file are ignored Instead trailing fif or raw fif is removed from the raw da
410. w2mat see Section 9 13 Alternatively the files can be read directly from Matlab using the routines in the MNE Mat lab toolbox see Chapter 10 The evoked data output can be easily read directly from Matlab using the fiff_load_evoked routine in the MNE Mat lab toolbox Both raw data and evoked output files can be loaded into mne_browse_raw see Chapter 4 MSH MNE CHAPTER 7 MSH MNE 7 1 7 2 Interactive analysis Overview Interactive analysis of the MEG EEG data and source estimates is facili tated by the mne_analyze tool Its features include 1 Viewing of evoked response data or data segments in a topographical layout 2 Alignment of MEG and head coordinate frames 3 Display of maps of the magnetic field and electric potentials 4 Computation and display of cortically constrained minimum norm current estimates and statistical maps derived from them The solutions can be displayed on folded and inflated cortical surfaces as well as on curved and flattened surface patches Fitting of current dipoles to the data 6 Connection to tkmedit part of FreeSurfer to display data on MRI Slices 7 Production of QuickTime movies and graphics snapshots in several image file formats 8 Connection to cliplab part of Elekta Neuromag software to produce graphics reports see Section 7 20 9 Inquiry and saving of source waveforms at selected surface points or within ROIs defined by label files 10 On line morphin
411. win dowing environment installed X11 is also needed by MNE For Mac OSX Leopard we recommend using XQuartz http xquartz macos forge org As of this writing XQuartz does not yet exist for SnowLeop ard the X11 included with the operating system is sufficient Testing the performance of your OpenGL graphics The graphics performance of mne_analyze depends on your graphics soft ware and hardware configuration You get the best performance if you are MSH MNE Installation and configuration c MSH MNE using mne_analyze locally on a computer and the hardware acceleration capabilities are in use You can check the On GLX item in the help menu of mne_analyze to see whether the hardware acceleration is in effect If the dialog popping up says Direct rendering context you are using hard ware acceleration If this dialog indicates Nondirect rendering context you are either using software emulation locally rendering to a remote dis play or employing VNC connection If you are rendering to a local dis play and get an indication of Nondirect rendering context software emulation is in effect and you should contact your local computer support to enable hardware acceleration for GLX In some cases this may require acquiring a new graphics display card Fortunately relatively high perfor mance OpenGL capable graphics cards very inexpensive There is also an utility mne_opengl_test to assess the graphics perfor mance more quantitati
412. with the same name as the BEM geometry spec ifications with the ending bem sol fif These files also contain all the information in the bem fif files After the BEM is set up it is advisable to check that the BEM model meshes are correctly positioned This can be easily done with by loading the COR fif file from mri T1 neuromag sets into MRIlab and by subse quently overlaying the corresponding pnt files using mport Strings from the File menu Tip The FreeSurfer format BEM surfaces can be also viewed with the tkmedit program which is part of the FreeSurfer distribution Tip If the SUBJECT environment variable is set it is usually sufficient to run mne setup forward model without any options for the three layer model and with the homog option for the single layer model If the input files are FreeSurfer surfaces surf and ico 4 are required as well Tip With help of the nosol option it is possible to create candidate BEM geometry data files quickly and do the checking with respect to the anatomical MRI data When the result is satisfactory mne_setup_forward_model can be run without nosol to invoke the time consuming calculation of the solution file as well Note The triangle meshes created by the seglab program have counter clockwise vertex ordering and thus require the noswap option Note Up to this point all processing stages depend on the anatomical geometrical information only and thus remain identical acr
413. x axis is chosen to be parallel to one of the sides of the magnetometer coil For planar sensors the z axis 1s likewise normal to the coil plane and the x axis passes through the centerpoints of the two coil loops so that the detector gives a positive signal when the normal field component increases along the x axis Table 5 2 lists the parameters of the normal coil geometry descriptions Table 5 3 lists the accurate descriptions For simple accuracy please con sult the coil definition file see Section 5 8 4 The columns of the tables contain the following data 1 The number identifying the coil id This number is used in the coil descriptions found in the FIF files Description of the coil Number of integration points used The locations of the integration points in sensor coordinates Weights assigned to the field values at the integration points Some for mulas are listed instead of the numerical values to demonstrate the principle of the calculation For example in the normal coil descrip tions of the planar gradiometers the weights are inverses of the baseline of the gradiometer to show that the output is in T m Mm BW dN Note The coil geometry information is stored in the file MNE_ ROOT share mne coil_def dat which is automatically created by the utility mne_list_coil_def see Section 5 8 5 is Bessrnton o m fw 2 Neuromag 122 2 8 1 0 0 mm 1 16 2mm planar gradiometer 3012 Vectorview type 1 2
414. x output files e Neuromag processing history is included with the output files mne_epochs2mat This new utility extracts epochs from a raw data file applies a bandpass filter to them and outputs them in a format convenient for processing in Matlab see Section 9 14 mne_analyze The following new features have been added 337 D Release notes D 2 5 D 2 6 D 2 7 D 2 8 338 1 Processing of raw data segment and easy switching between multiple evoked data sets not in the manual yet 2 Sketchy surface display mode for source spaces with selection triangu lation information created with the ico option t mne_setup_source_space 3 Rotation of the coordinate frame in the coordinate system alignment dialog see Section 7 16 4 Several new graphics output file formats as well as automatic and snap shot output modes see Section 7 8 8 5 It is now possible to inquire timecourses from stc overlays Both labels and surface picking are supported 6 Added an option to include surface vertex numbers to the timecourse output see Section 7 13 3 1 7 Overlays matching the scalp surface can now be loaded see Section 7 14 8 The dipole display dialog has now control over the dipole display prop erties Multiple dipoles can be now displayed see Section 7 15 3 9 Time stepping with cursor keys has been added 10 Dynamic cursors have been added to the full view display 11 The viewer display now automatically ro
415. xyz Calculate the square sum of the three Cartesian compo nents of several vectors listed in one row or column vec tor Compose a file name relative to MNE_ROOT mne_find_channel Find a channel by name from measurement info mne_find_source_space_hemi Determine whether a given source space belongs to the left or right hemisphere mne_make_combined_event_file Combine data from several trigger channels into one event file mne_omit_first_line Omit first line from a multi line message This routine is useful for formatting error messages mne_prepare_inverse_operator Prepare inverse operator data for calculating L2 mini mum norm solutions and dSPM mne_setup_toolbox Set up the MNE Matlab toolbox mne_transform_coordinates Transform locations between different coordinate sys tems This function uses the output file from mne_collect_transforms described in Section 9 9 as input mne_transpose_named_matrix Create a transpose of a named matrix Table 10 13 Utility functions MSH MNE 259 10 The Matlab toolbox mne_transform_source_space_to Transform source space data to another coordinate frame Table 10 13 Utility functions mne_ex_average_epochs Example of averaging epoch data produced by mne_epochs2mat see Section 9 14 Example of noise cancellation procedures mne_ex_compute_inverse Example of computing a L2 minimum norm estimate or a dSPM solution Example of listing evoked response data sets mne_ex_evo
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MNE software User`s Guide - Martinos Center for Biomedical Imaging

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