"user manual"
Contents
1. 16 Installing the module seen enne 16 p dson widget vise ERES IC sdei S 16 Add PCA fields Ment isset eterne 17 SSD m 18 Gener l Description sis Oe ERRAT 18 Installing the module sss 18 Using ssp liligi casse e HR ette Pe den RS 19 Activating VectOFs suse ge e ee e e RR 19 Clearing active vectors 20 Deactivating projections temporarily 20 Description Of the menus ener 20 Filem ni uda oie 20 Edit MeN sit AC e t e poe 21 Module revision history 22 Std SEle GEIUTS gesta ea euet redde tisse 23 General Description sae re e ede eite ene boas 23 Installing the module 23 Menu description ees o RD et e PER RARE desde 23 std selections DHTE22 L is ti 24 General Description enne enne 24 Installing the module 24 Sel CtiORs iaia ret t c b et ed e tea 24 std selectiols VV aten eats 26 General Description eene 26 Installing the module 26 Selections eerie nd 26 templates E 29 General Descriptions ise oett ee Re e IE 29 Installing the module 29 UserinterfQGG uias 29 etsen ls 32 General Description 32 Installing the module 32 Lisp interj e aes o RE RU ETE tented 32 Module revision history 33 XII Ee 35 General Description2. 35 Installing the module 35 ssi ee 33 Lisp interf ce rd bh er 36 Module revision history gt 37 XPIOMEE T2 resis cent ee 38 General Description 38 Installing the module 38 User interface E ERR E aca Er EN EP GER SERE eM 38 Lisp interface uo ee P HERES RENE 38 Module revision history 39 Introduction Part 1 Module Reference This part of the manual contains variable reference information It starts with reference of utility Lisp modules delivered with the program The following modules are described batch processor A module that provides an easy way to perform some procedures automatically on several files and measurements channel selection Enables easy definition of channel sets and creation of channel selection menus classify by table Classifier function for off line averager which allows category definitions through a relatively simple configuration file pca This module performs principal component analysis on data ssp Signal space projection utility that can be used to manage vectors that describe sub spaces for projection operations std selections Utility for easy selection of standard channel sets to the main window std selections nm122 Standard channel selections for Neuromag 122 std
3. Rack A MEG channels 7 834129 10 5 6 29 30 25 26 21 22 17 18 13 14 27 28 23 24 19 20 15 16 11 12 Rack B MEG channels 32 31 36 35 40 39 44 43 48 47 34 33 38 37 42 41 46 45 50 49 52 51 56 55 60 59 54 53 58 57 Rack C MEG channels 66 65 70 69 62 61 64 63 68 67 74 73 78 77 82 81 86 85 90 89 72 71 76 75 80 79 84 83 88 87 Rack D MEG channels 107 108 103 104 99 100 95 96 91 92 109 110 105 106 101 102 97 98 93 94 117 118 113 114 119 120 115 116 111 112 121 122 25 SEMEN std selections vv 1 8 STD SELECTIONS VV General Description Installing the module Selections The package std selections vv provides definitions for standard channel sets suitable to be used with Elekta Neuromag and Vectorview devices It contains essentially data and provides no functions or variables See also channel selection lsp and std selections Isp The module is supplied with the Graph version 2 93 and later in the stan dard module library neuro lisp graph lt version gt lib and to load the code into the system you need to give lisp command require std selections vv After this command the functionality of the module should be available Note however that the setup files that are used to save Graph state are capable to load the code automatically if the module was present when the setup was made Is such case loading the setup will load the module and the require command is not necessary The following chann
4. It is a good idea to include all relevant information that is needed to use the code The second form if gt length args 2 warn batch average Too many arguments s args just checks that there are not too many arguments In the let construction suitable local variables are set using the argument values or to default val ues if the argument is not available let start or first args 10 end or second args 10000 lt code gt Then finally we get to the actual code open diskfile file average start end save average output Signal Processor batch processor 1 4 Module version history This code does the following things 1 it opens a diskfile defined by the argument file 2 It executes the averaging command using the given or defaulted start and end time value 3 It saves the result of averaging to file defined by the parameter output Main new features modifications in the module Version 1 4 Removed direct references to directory neuro This allows usage also when software is installed to a nonstandard location Version 1 3 package rev 1 2 2 Modified filename handling to make module to work in Linux systems Version 1 2 Added edit buttons to edit configuration files easily Allows using nil as the setup name and thus preventing loading any setup This is useful if one wants to run the batch with different setups Version 1 1 Initial version chann
5. The definition for the states of the signal processor that should prevail dur ing processing is given by its name in the batch dialog The definition itself should reside in file user lisp root batch states name lsp User interface Filter neuro data test O Direc Files jn audo 1 bdip jn_aud0 1 fif jn_aud0 1 dipoles xfit 5 5 1 fif jn_aud0 1_dipoles fif jn_aud0 1_raw fif jn_aud0 1_raw_ssst fif Arguments Selection a test 060515 jn aud01 rawS2 fif Add Filter Close Help batch processor 1 4 where lt name gt matches to the name of the state definition and lt user lisp root gt denotes the root directory of users private lisp code One definition file can define arbitrary number of signal processor states each of which is realized before the actual processing routine is invoked It can define for example three different states which cause averaging process to average triggers one two and three Each file is then averaged three times produc ing three output files one for each trigger The exact format of the state definition files is given in State description syntax on page 6 The definition of the process that is to be applied for each file in each state of the processing system is also defined by its name in the batch dialog The actual code that is executed should be in lt user lisp root gt patch processes lt name gt 1sp in similar manner as a the state fi
6. Typically these forms alter resources of some widgets or values of user parameters affecting the processing Typical example would be to set averager trigger channel or tune filter settings Second modification entry type is a notation to form combinations of sim ple modifications Its syntax is lt combination modification gt combine lt sm gt lt sm gt lt sm gt where lt sm gt stands for lt simple modification gt This form takes several lists of simple modifications This syntax corresponds writing all combi nations of modifications so that one simple modification is taken from each of the lists and these are merged together The merging is done so that the file extensions are concatenated to form a new combined exten sion and forms are concatenated to apply all the modification commands If the definition is for example combine A resource G widget filter pass band band pass 8 12 B resource G widget filter pass band band pass 15 25 51 setu trigger source threshold 0 S2 setu trigger source threshold 1 Then this is equivalent of giving the simple modifications Process definition syntax 51 resource 8 12 setu 0 AS2 resource 8 12 setu 1 BS1 resource 15 25 setu 0 BS2 resource 15 25 setu 1 The process definitions are essentially normal functi
7. adding the vector User will be prompted to give a name to this new vector Vector names need not to be unique but having multiple vectors with same name is likely to case confusion Version 1 7 0 ssp remove space Moved list refresh to the beginning to ensure the list is updated also when errors occur ssp lsp ssp save file Uses now add_proj_namelist to add the channel names Requires that the utility exists Wrapped add_proj_namelist with utility program to make it installation root independent ssp load file ssp vector dir template Handle missing neuro ssp direc tory cleanly 22 Signal Processor std selections 1 6 STD SELECTIONS General Description Installing the module Menu description The package std selections provides an interface for easy selection of standard channel sets to the main display It adds a new submenu Selec tions into the Displays menu This menu contains a button for each pre defined selection Note that the menu is a tear off menu so that it can be lifted on the workspace for handy operation This package uses a pick widget called pick to select the channels and links it automatically to widget display This means that it is only useful with setups that contain these two widgets in suitable places The input to the pick widget can be freely chosen However the output of the widget is linked into widget display every time the selection is changed The
8. again The name of the event tag table is setup specific and is set through the Parameters menu The file is not reloaded automatically if you make changes to it After changes you should issue load complete filename or load filename with no lsp The second simpler forms requires that the directory where the table is is in the search paths of the program Debugging There is a handy way to debug the working of the classifier Since it sim ply takes one argument it can be easily tested on command line Simply call the function with some time classify by table lt time gt and see what is the opinion of the routine Even handier is use classify by table first x selection Then you can use mouse to point the time points Module revision history Changes to the module Version 1 2 1 Technical repackaging no changes to the code Version 1 2 0 classify by table lsp Removed the dependency to module trigger utils by copying the get stimulus combination into the file as cbt get stimulus combination 15 1 4 PCA General Description Installing the module pca on widget The package pca provides code for applying principal component analy sis on widget data It exports function pca on widget which does the task It also co operates with the module SSP so that the menu Actions in the SSP dialog will contain buttons for easy access to PCA vectors This package is capab
9. basic setup provided in the examples directory provides an example setup that works with the module The std selections module is supplied with the Graph version 2 92 and later in the standard module library neuro lisp graph lt version gt lib and to load the code into the system you need to give LISP command require std selections After this command the functionality of the module should be available Note however that the setup files that are used to save Graph state are capable to load the code automatically if the module was present when the setup was made Is such case loading the setup will load the module and the require command is not necessary This module uses module channel selection std selection nm122 std selection vv to create the menu See the reference of these modules for details of the selections 23 SEMEN std selections nm122 1 7 STD SELECTIONS NM122 General Description The package std selections nm122 provides definitions of standard channel sets suitable to be used with Neuromag122 device It contains essentially data and provides no functions or variables See also channel selection lsp and std selections lsp Installing the module The module is supplied with the Graph version 2 93 and later in the stan dard module library neuro lisp graph lt version gt lib and to load the code into the system you need to give LISP command require std selections nm122 After t
10. fit selected point are used xfit program Variable containing the start up command used to start a Xfit process xfit pick selected point Function that shows current selected time point using Xfit See menu button Pick selected point above xfit timeout Variable defining the timeout value of the communica tion link xfit transfer data Function that shows arbitrary data using a Xfit Manipulating xfit channel selections is unfortunately somewhat compli Cc a ated due to usage pattern of Xift which is oriented towards manual oper tions Selections to use must be first defined and the taken into use Further complication is that selection are done using logical channels Following functions are available xfit selection clear Clear Xfit channels selection 36 Signal Processor xfit 1 5 Module revision history e xfit selection add Add selection into collection of channel defini tions e xfit selection use Use a predefined channel definition or define and use a new one xfit selection omit Make Xfit to forget one selection definition e xfit selection set Set xfit channel selection As a side effect the selection is added to the selection definitions in Xfit e xfit loadsel Load a selection from a file Summary of changes xfit 1 5 Maintenance changes to remove explicit references to directory neuro xfit 1 4 Added routines to manage xfit channel
11. selections Fit command did not function if selection was not restricted xfit 1 3 Fitting can be restricted to use only a set of channels Current working directory of graph is transferred to xfit after data transfer Allows easier saving to the source directory 37 1 12 XPLOTTER 1 2 xplotter 1 2 General Description Installing the module User interface Lisp interface The package xplotter provides an interface for managing slave Xplotter programs It provides a menu to make data transfers from Graph to Xplot ter easy It also provides functions that enable a command widget to behave as if it was a display widget having Xplotter functionality Note that the xplotter menu is a tear off menu so it can be lifted on the desktop This module is available in standard module library of Graph so that you can load it by command require xplotter Note that setup files are also capable to load this module so that if your current setup provides the module you don t need to enter the command When loaded the this module creates a submenu called xplotter into the Displays menu The actions performed by the buttons in the xplotter menu are described below Start xplotter This button starts a Xplotter program for viewing data unless it is already started So only one Xplotter can be managed using the menu Show selection Before using this button user should select some time interval on some of the di
12. 421 2641 2621 2631 left parietal mags MEG channels 631 421 411 711 431 441 741 1821 1811 1831 1841 1631 2011 right parietal mags MEG channels 1041 1111 1121 721 1141 1131 731 2211 2221 2241 2231 2441 2021 left occipital mags MEG channels 2041 1911 2111 1921 1941 1641 1931 1731 1721 2141 1741 1711 right occipital mags MEG channels 2031 2311 2341 2321 2431 2121 2331 2511 2521 2131 2541 2531 left frontal mags MEG channels 521 511 311 341 121 821 531 541 321 611 331 621 641 27 R std selections vv right frontal mags MEG channels 811 911 921 1211 1221 1411 941 931 1231 1011 1021 1241 1031 28 Signal Processor templates 1 9 TEMPLATES General Description Installing the module User interface The package templates provides an interface for managing a template filter The template filter it uses must have name template Loading the module will also create the widget if it does not exists or has wrong type It provides a menu for easy creation and manipulation of the templates but it does not define what to do with the template output itself For evaluation of this module a setup called template search is provided in the exam ples directory The menu provided is created as a submenu of the Com mands menu Note that the menu is a tear off menu so it can be lifted on the desktop See Using menus in Graph User s Manual This module is available in standard module l
13. Clear files button Pressing the button when no files are selected clears all entries Below the file list is a text field for output directory Pressing the Output directory button pops up a file selection box that allows you to select the directory easily You may enter the directory also using keyboard Press ing button Output to source dir sets the output directory to source so that output files will be created to the same directory as the corresponding source file The lower part of the batch dialog contains text fields for names of state definition and the process definition You can enter them either by key board or by pressing the Select button in front of them Pressing it pops up a file selection box viewing the correct directory If the batch code directories do not exist program asks user whether it can create them Answer yes if you want them to be created The directory will be empty except of a directory file that is a symbolic link to the directory containing example code provided with the system You can create a new definition file by clicking the New button This pops up a file selection box where you should enter the name of the file to be created After you have given the name the file will be created and a tem plate description will be written into it Comments in template code describe also the syntax of the file so it is sort of self documenting If you give name of an existing file the program asks somewhat mis
14. Elekta Neuromag Signal Processor Reference manual Software version 2 94 October 2008 ELEKTA Manufacturer Elekta Neuromag Oy Siltasaarenkatu 18 20 A FIN 00 530 Helsinki Finland Tel 358 9 756 2400 Fax 358 9 756 24011 Web www elekta com Copyright 1996 2008 Elekta Neuromag Oy Helsinki Finland This document contains copyrighted and possibly confidential information and is intended for the exclusive use of customers having Neuromag products and authorized representatives of Elekta Neuromag Oy Disclosure to others or other use is strictly prohibited without the express written authorization of Elekta Neuromag Oy Elekta Neuromag Oy reserves the right to make changes in the specifications or data shown herein at any time without notice or obliga tion Elekta Neuromag Oy makes no warranty of any kind with regard to this document and the related software including but not limited to the implied warranties of merchantability and fitness for a particular purpose Elekta Neuromag Oy shall not be liable for errors contained herein or direct indirect incidental or consequential damages in connection with the furnishing performance or use of this material and software Printed in Finland Printing History Neuromag p n Software Ist edition DA10240 4A 2 92 2nd edition NM10240A A 2 93 3rd edition NM10240A B 2 94 Date October 1996 December 2004 2008 10 09 Signal Processor CONTENTS In
15. Modified event structure Events now can contain properties which are dynamically defined trigger utils 1 6 e Added re trigger option e Added get length key to find out the length of the trigger e Routine make event now accepts length of the event trigger utils 1 5 e Added context variable to map events This allows recursive calls Map events now shows the event tags in working dialog e Classifier can be passed to map events trigger utils 1 4 Minor internal modifications 33 R trigger utils 1 9 trigger utils 1 3 Minor internal modifications trigger utils 1 2 Added routine time span available p Added key polarity to map events trigger utils 1 1 Initial version 34 Signal Processor xfit 1 5 1 11 XFIT 1 5 General Description Installing the module User interface xfit Tear off The package xfit provides an interface for managing a slave Xfit pro gram It provides a menu to make data transfers from Graph to Xfit easy Note that the xfit menu is a tear off menu so it can be lifted on the desk top This module is available in standard module library of Graph so that you can load it by command require xfit Note that setup files are also capable to load this module so that if your current setup provides the module you don t need to enter the command When loaded the this module creates a submenu called xfit into the Dis plays menu The act
16. ains e g thresholded response signals Then the event is classified as S3ab if there is a response both before and after the event Second class would be the epochs when the response is only either before or after the trigger point The entries from fourth to ninth are to classify the ordinary triggers where they are delivered to one trigger line at a time The last entry matches to anything and is recommended Developing a setup In order to have a functional system we need a setup which has trigger combinations available You can start from a simple basic averaging setup and replace the threshold widget by a encode widget The output of the encode has the trigger channels combinations as data values If you analyze Neuromag 122 data and you need to condition the tagging to spe cific trigger lines you also need to have the threshold widget present to create clean singe trigger lines In Vectorview this is not necessary since the triggers are not analog signals The triggers used in conditioning can be created from any source by thresholding properly maybe with some preprocessing 14 classify by table 1 2 Signal Processor Verify that the setup works with these simple settings It should average everything into one category Then add classify by table into the Parameters gt averager gt average classify and change the tag in the aver age widget to match something that is known to exist on the data Then try
17. at shows arbitrary data using a Xplotter Both replacing the existing data and overlay are supported e xplotter show selection Function that shows current selection using default Xplotter e xplotter timeout Variable defining the timeout value of the com munication link Changes to the module xplotter 1 2 Xplotter interface for loading data now includes option overlay It allows overlaying old data instead of replacing it 39 ELEKTA Elekta Neuromag Oy Siltasaarenkatu 18 20 F1 00530 Helsinki Finland Tel 358 9 756 2400 Fax 358 9 756 24011 Web www elekta com
18. by table provides an utility that allows relatively easy way to classify epochs It is intended to be used with the off line averager utility The module consists of a single Lisp routine classify by table and an example classification table The routine attempts to classify an epoch at the time point given as a parameter This documentation assumes that the user knows the basic operations and scripting needed for using the signal processor program For details of such operations refer to Graph Users Guide This module is available in graph 2 94 and later or it can be provided sep arately It is dependent on module trigger utils which must be present You can test its presence by trying command require trigger utils and see if it succeeds or fails The module itself is also loaded with require classify by table No example setup files are provided Variable event tag table name is added into the Parameters menu param eter class classification The routine has an interface that matches the calling convention of the classifier function of the off line averager It can thus be used as such It takes only a single parameter which is the trigger time in x units typi cally seconds of the epoch All other settings are given indirectly through a table on the disk How the averager uses the classifier When the averager parameter average classify is set the value is assumed to be a name of a function When a trigger poin
19. current threshold value in unary widget defined by user variable template threshold by 1 1 Threshold up 2x This button multiplies the current threshold value in unary widget defined by user variable template threshold by 2 0 Threshold down 10 This button multiplies the current threshold value in unary widget defined by user variable template threshold by 0 9 Threshold down 2x This button multiplies the current threshold value in unary widget defined by user variable template threshold by 0 5 30 Signal Processor templates Show current Activation this button will select using x selection of the main display the time span of the origin of the current template It will also move the view to show it 31 trigger utils 1 9 1 10 TRIGGER UTILS 1 9 General Description Installing the module Lisp interface The package trigger utils provides utilities for managing events It pro vides basic functions to create events access their properties and to scan widget data to find events Using event manipulation routines in this mod ule are recommended in order to keep the internal representation of event descriptions coherent in all modules This is purely scripting utility No user interfaces are provided This module is available in standard module library of Graph so that you can load it by command require trigger utils Note that setup files are also capable of loading this module so that
20. d since then the batch would need continuous attention You can however still scroll the log window since this runs independently of the main program To view the log file use the scroll bar on the right side of the text area When the batch starts the log dialog shows the end of the log and scrolls automatically forward when new log messages appear However if you use the scrollbar to view the file The automatic scrolling is then suppressed so that you can examine the text To activate the automatic scrolling again move the view to the end of the file Note that the color of the trough of the scrollbar changes when the automatic scrolling is on Running a batch also creates a log file lt user lisp root gt batch logs Batch date time log where date is in format yymmdd and the time in hhmmss The date and the time tell the time when the batch was started The log files are never deleted automatically so you should clean up the log directory ever now and then The batch processor expects currently that all input and output files are fiff format files having extension fif in their names Using files having some other naming convention is possible but the automatic test utility is not able to anticipate such an action Same applies to cases where process ing code produces output files having different name than the one that was given to it or if it produces multiple files State descriptions should be in directory user lisp
21. efinition column vectors must match the number of input channels fed into ssp widget Otherwise the widgets do nothing You can see the description of the pool vectors if any by double clicking the name of the projection To enter a description see Edit menu on page 21 One can activate a definition in the vector pool by selecting it and the pressing the button between the selection boxes that has a right arrow Selecting a definition is achieved by clicking its name in the selection box You may also select multiple entries at a time by dragging the cursor or by pressing SHIFTkey while selecting Pressing the SHIFTkey makes selec tion state to toggle when an item is clicked Activating an item causes it to appear on the active vector selection box and the new set of active vectors is installed to widgets 19 Clearing active vectors Deactivating projections temporarily Description of the menus File menu ssp To clear the current active vectors press the Clr button Your confirmation for the clearing will be asked before the actual deletion Note that nor mally you don t lose the vectors if you clear the active vectors since when the pool vectors are activated they are copied rather than moved to the active vectors You loose definitions only when you delete pool vectors The transformations can be set temporarily off by pressing the Off button between the selection boxes The active vectors are kept in
22. el definitions apply to channel names left temporal MEG channels 223 222 212 213 133 132 112 113 233 232 242 243 1513 1512 142 143 1623 1622 1612 1613 1523 1522 1542 1543 1532 1533 right temporal MEG channels 1313 1312 1322 1323 1443 1442 1422 1423 1343 1342 1332 1333 2613 2612 1432 1433 2413 2412 2422 2423 2643 2642 2622 2623 2632 2633 left parietal MEG channels 632 633 423 422 412 413 712 713 433 432 442 443 742 743 1823 1822 1812 1813 1833 1832 1842 1843 1633 1632 2012 2013 right parietal MEG channels 1042 1043 1113 1112 1122 1123 722 723 1143 1142 1132 1133 732 733 2213 2212 2222 2223 2243 2242 2232 2233 2443 2442 2022 2023 26 Sig nal P rocessor std selections vv left occipital MEG channels 2043 2042 1913 1912 2112 2113 1922 1923 1942 1943 1642 1643 1933 1932 1733 1732 1723 1722 2143 2142 1742 1743 1712 1713 right occipital MEG channels 2033 2032 2313 2312 2342 2343 2322 2323 2432 2433 2123 2122 2333 2332 2513 2512 2523 2522 2132 2133 2542 2543 2532 2533 left frontal MEG channels 522 523 512 513 312 313 342 343 123 122 823 822 533 532 543 542 323 322 612 613 332 333 623 622 643 642 right frontal MEG channels 812 813 912 913 922 923 1212 1213 1222 1223 1413 1412 943 942 933 932 1233 1232 1012 1013 1022 1023 1242 1243 1033 1032 left temporal mags MEG channels 221 211 131 111 231 241 1511 141 1621 1611 1521 1541 1531 right temporal mags MEG channels 1311 1321 1441 1421 1341 1331 2611 1431 2411 2
23. el selection 2 0 1 2 CHANNEL SELECTION 2 0 General Description Installing the module Functionality The package channel selection provides an library utility for easy selec tion of standard channel sets to a display It supersedes the functionality that used to be provided by module std selections which is now rewrit ten to use this module Code can add a new submenu into desired menu This menu contains one button for each predefined selection channel set and a submenu that has set of channels sets When a new channel set is selected from the menu the channel list is inserted into a pick widget defined at the creation time of the menu The pick widget is then linked into a display defined also at the creation time of the menu Note that the menu is a tear off menu so that it can be lifted on the work space for handy operation The channel selection module is supplied with the Graph version 2 93 and later in the standard module library neuro lisp graph lt version gt lib and to load the code into the system you need to give LISP command require channel selection After this command the functionality of the module should be available Note however that the setup files that are used to save Graph state are capable to load the code automatically if the module was present when the setup was made Is such case loading the setup will load the module and the require command is not necessary In additi
24. es the tag Second element describes the trigger combina tion that must be present on the trigger line Here the combination is assumed to be encoded into the height of the trigger signal as the binary combination of the trigger bits Rest of the elements define extra conditions that must prevail Currently there are provided two combinations signal lt widget name gt lt channel number gt lt begin gt lt end gt no signal widget name channel number begin lt end gt These definitions cause function to examine the signals at specified widget channel time range The channel count starts from 1 and the epoch is relative to the trigger point 13 classify by table 1 2 Below is an example file 17 This is a sample event tag table 7 Comments can be entered in normal lisp fashion mr event tag tabl Most specific entries first Note that the second element is trigger combination but the third element in signal is channel number S3ab 4 signal stim 1 1 0 2 0 signal stim 2 1 0 0 05 signal stim 1 1 0 2 0 signal stim 2 1 0 0 05 other any The first three classes are conditioned by presence of signals in the outputs of widget signal The records are examined one by one until a match is found Therefore ones need to put the most specific conditions first One could imagine that the example the channels of stim cont
25. est to use fiff files since both Xfit and Graph can read them Load To load a file containing projections select Load in the File menu of the ssp dialog A file selection box will pop up Use this box to select which file you want to load Program is capable to load projections both from a Lisp file and from a fiff file Close Activating this button will close the ssp dialog 20 Signal Processor ssp Edit menu Delete selected Activating this button will delete all selected entries from both vector pool and active vectors It will ask confirmations before deleting When you select items to be deleted check that there are no items selected on the other selection box Add to SSP When this button is pressed the currently selected vectors in vector pool are activated that is they are added into the current projections The vectors will also be copied to the selection box showing the active vectors Clear SSP Selecting this button will clear all active ssp vectors Explode When this button is activated all selected projections in the pool are exploded This means that if the dimension of the projection space is larger than 1 which means that the definition is a matrix rather than a vector this matrix is replaced by set of separate vectors that are the col umn vectors of the matrix For the reverse operation see the Implode button Implode Activating this button will take all selected spaces i
26. his command the functionality of the module should be available Note however that the setup files that are used to save Graph state are capable to load the code automatically if the module was present when the setup was made Is such case loading the setup will load the module and the require command is not necessary Selections The following channel definitions apply to channel names This means that the channel numbering presented here starts from1 not from 0 as the channel location numbers in selectors vertex MEG channels 13 14 15 16 49 50 51 52 53 54 61 62 63 64 65 66 73 74 89 90 99 100 117 118 119 120 121 122 left temporal MEG channels 43 44 45 46 47 48 49 50 55 56 57 58 59 60 61 62 67 68 69 70 71 72 73 74 right temporal MEG channels 123456789 1011 12 13 14 111 112 113 114 115 116 117 118 119 120 left parietal MEG channels 47 48 49 50 51 52 59 60 61 62 63 64 71 72 73 74 79 80 87 88 89 90 right parietal channels MEG channels 5 6 11 12 13 14 15 16 97 98 99 100 109 110 115 116 117 118 119 120 121 122 24 Sig nal P rocessor std selections nm122 occipital channels MEG channels 75 76 77 78 79 80 81 82 83 84 85 86 91 92 93 94 95 96 101 102 103 104 105 106 107 108 109 110 frontal MEG channels 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 EEG 1 EEG channels 123456789 10 11 12 13 14 15 16 EEG 2 EEG channels 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
27. ibrary of Graph so that you can load it by command require templates Note that setup files are also capable to load this module so that if your current setup provides the module you don t need to enter the command Descriptions of the actions provided by the menu are listed below Note also that the Parameter menu will contain an editor for several user parameters defined by this module The name of the parameter group is Template search Set Template This button provides a submenu that contains several ways to set the active template in the template filter template In the beginning there are two buttons in it namely From selection and From average The buttons are described below From selection Before selecting this button you should select a time span from a the display This selection defines the template we are going to install Activating this button will take data from widget defined by user parameter template source and installs it into the template widget Typically this user parameter should contain the name of a widget that carries filtered MEG data From average Activating this button will take the current average which has to be stored in widget average and installs it into template widget You can also use only a portion of the average data by selecting part of it in a display that is connected to it 29 templates Saved template If a template has been saved during a sess
28. if your current setup provides the module you don t need to enter the command This section describes briefly what functionality is available For detailed information on the functions use on line descriptions of the functions Events are currently described by association lists that is lists that contain property value pairs However the event data should not be accessed directly Using the routines here allows later changes to the event objects without rewriting the code that uses the event data For basic creation and manipulation of events the following functions are provided e make event Create an event event time Return time of an event event class Return event class of an event event length Return length of an event if any event set property Set an arbitrary property of an event event get property Return an arbitrary property of an event To scan data and create event objects from events in the data following utilities are available First following variables define the default values that are used when no explicit value is given to the functions default trigger source Trigger channel to be scanned for events In normal averaging applications this is usually a channel which have the triggers encoded as numbers but it can also contain analog signals if the triggering modes are set suitably e default classifier Default classifier function Classifiers functions are used to classify events The
29. ion a new button to load and activate this template is created into this menu These buttons have the name of the template on them Save template Activating this button will save the current template That is the tem plate that was last activated Program will pop up a file selection box that allows you to save the template in fiff format file Note however that the extension used with templates is not fif but tpl The exten sion will be added automatically if you don t provide it explicitly When you save a template a new button will be added into the Set template menu This button will automatically load and install the template Load template Selecting this button you will pop up a file selection box that enables you to load and activate a template Note that the template files have name extension tpl Set search point Before using this button set a zero length x selection into a suitable place Activation the button will set this time into the search pointer for template searches Next search will then start from this point Next match This action will scan the channel defined by user variable template out put until it finds a positive pulse It sets the search pointer to the time of the first local maximum after the start of the pulse It also alters the x selection and the current view of the main display so that the trigger point is visible and selected Threshold up 10 This button multiplies the
30. ions performed by the buttons in the xfit menu are described below Start Xfit This button starts a Xfit program for viewing data unless it is already started Only one Xfit can be managed using the menu Transfer selection Before using this button user should select some time interval on some of the displays See Selecting time intervals in the Signal Processor Users Manual Activating this button will transfer data in widget defined by the user variable default data source within the selected time span to the Xfit program It also performs an autoscale operation Pick selected point Before using this button user should select a single time point on some of the displays Activating this button will transfer a range of data around the selected point into the Xfit process and Xfit is told to select the same time point The length of the data transferred is defined by user variable xfit region width that is available also through Parameters menu button Misc defaults If the selected point is within data that is currently transferred into Xfit no data is transferred only the new time point is picked Fit selected point Before using this button user should select a single time point on some of the displays Activating this button will transfer a range of data around the selected point into the Xfit process and Xfit is commanded 35 Lisp interface xfit 1 5 to fit a dipole to this particular time point The de
31. jections but in the multi source model they are taken into account Matrices are handled the same way as a list of column vectors They provide however a handy way to group related vectors so that they can be used as a single object When loaded the module creates a suppressor widget called ssp unless it already exists All operations apply automatically to this widget so to use the module in sensible way it should be used with a setup that con tains the ssp widget in reasonable environment The data connected into the ssp widget should contain only the channels that used in the projec tions Typically this means that all MEG channels are coupled in it When selected space is activated a related matrix is installed automati cally to two other widgets too provided that they exist They should be linear widgets Into widget removed code assembles a set of orthonor mal basis vectors that span the defined subspace Use how you like In widget timevar it installs the solution matrix to calculate the amplitudes related to the original space definition vectors so that multiplying the vec tors with these amplitudes would produce vector that matches best in sense of an euclidean norm to the input vector So this widget has in its output the time variations of the sources in a multi source model where sources are defined by given field shapes These last two widgets are not created automatically If they are needed
32. k to a predefined set of channels It takes the name string of the desired device type and the name of the selection The selection must be earlier defined by using define channel selections Command uses given pick and display widgets The pick widget defaults to widget pick and the display defaults widget display Version 2 0 2 2008 03 28 Technical repackaging no changes Version 2 0 1 not released Moved std selections lsp to sub directory config since it really is more like a configuration file channel selection lsp Set default device to Vectorview Version 2 0 0 std selections lsp This now contains only requires of NM122 and Vector view selections Bumped to version 2 0 to denote that this is now official Vectorview version channel selection lsp use pick selection Display can be now nil allows calling without any specific display widget Added a hook function to allow later definitions of actions to be performed when a selection is made Useful to update name labels etc std selections vv lsp std selections 204 lsp Corrected channel pair order ing from prototype order to production version std selections 204 lsp Removed definition for nm122 Corrected error in left parietal Version 1 0 Initial version 11 classify by table 1 2 1 3 CLASSIFY BY TABLE 1 2 General Description Installing the module Setup files provided User interface Technical details Classify
33. le Process definition is essentially a LISP program that has to obey some formal constraints The syntax of the file is given in Process definition syntax on page 7 The batch processor has a friendly interface dialog that can be popped up from button Batch in the Commands menu The dialog is shown in fig ure below File list neuro data test 0605 15 jn_aud0 1_raw fif neuro data test 0605 15 jn_aud0 1 rawS 1 fif neuro data test 0605 15 jn_aud0 1_rawS2 fif Output directory source Add file Clear files Output directory Output to source dir Process definitions Select States H New Edit Select Process H New Edit At the top of the dialog there is a list showing all files currently selected to be processed To add a file into this list click the Add file button below the file list This pops up a file selection box Use the selection box to pick up the desired file For details about selection boxes see Using file selec tion boxes of Signal Processor Users Manual You may give the extra Signal Processor batch processor 1 4 Testing batches arguments to be passed to the batch process with the file in the text box above the file name field of the selection box Pressing Add button will not remove the dialog so that you can easily enter multiple files To remove it use the Close button In order to delete erroneous entries select the desired file names by cursor and press the
34. le to operate on data in any G widget so that it does not depend on the setup However it creates a new matrix source widget pca fields where it stores the PCA vectors representing the field expansion The pca module is supplied with the Graph version 2 92 and later in the standard module library neuro lisp graph lt version gt lib and to load the code into the system you need to give lisp command require pca After this command the functionality of the module should be available Note however that the setup files that are used to save Graph state are capable to load the code automatically if the module was present when the setup was made Is such case loading the setup will load the pca code too and the require command is unnecessary The function pca on widget has the following syntax pca on widget widget lt start time gt lt end time gt The parameter widget defines the source from which the data should be taken into the analysis It can either be a G widget or its name string The parameters lt start time gt and lt end time gt define the data span on which the analysis is performed They are expressed in real x units typi cally in seconds Function calculates the singular vectors of the data matrix corresponding to field shapes The singular vectors representing the time variation of the fields are not calculated If you need to know them use the SSP module with the PCA field vectors to dis
35. leadingly if itis OK to write over the existing file If you answer yes an editor will be opened editing the file and you can make changes to it You can edit the process or state definition file entered into a text field by pressing the Edit button on the right side of the text field After all the above mentioned four fields have been filled you can run the batch by pressing Run button at the bottom of the dialog It is however recommended that you first run a test run by clicking the Test button instead The test button runs a bare bones process that just checks that all input files can be opened test procedure uses the default disk file and assumes that the inputs should be normal fif files that none of the out put files already exist that the output files can be created and that they will be created only once so that some process steps will not write over previous results Test routine also realize all the different states of the processing system so that obvious mistakes in state definitions can be detected that is those that cause errors Running batches Restrictions State description syntax batch processor 1 4 To run a batch press the Run button at the bottom of the dialog The dia log will disappear and a log window will pop up Then the batch process starts You can not interact with the Graph program during the batch unless the batch process asks you to do something which is not recom mende
36. n vector pool and replaces them with a single matrix that contains all the basis vectors in the selected spaces The reverse operation is available using the Explode button Edit name Activation this button will open a dialog that enables you to give a new name to the selected vector Enter the new name into the text box and press OK Edit description Activation this button will pop up a simple text editor with the current description text of the vector You can change the text freely The description need not be a single line Remember that the vector defini tion and the comment are lost unless you save the entry into a file Actions menu This menu is reserved for all kinds of commands to obtain new vectors By default it contains only one button Pick selected field but other modules may create more buttons into it 21 Module revision history ssp Pick selected field Before activation this button you should select a time point from one of the displays The length of the time should zero that is click a single line into the display For making time selections see Selecting time intervals in Signal Processor User s Manual When the button is activated a sample vector is taken from the current output of the ssp widget at the time specified by the current selection This vector will be added into both pool and active vectors and if the projections are temporarily off they will be turned on again Before
37. on definitions They just have to adhere to some specific conventions The syntax is as follows define batch process name amp keys file output args Comment string form Example process definition batch processor 1 4 These functions are defined by define batch process instead of defun The argument list must match conventions used by the batch processor but otherwise the code can do what ever is needed The arguments passed to the process during batch are following e file String containing the full pathname of the input file output String Containing the full pathname of the output file args List of arguments that were given with the input file There is a sample averaging batch process in directory examples under your batch process directory The code of the routine is listed below define batch process average amp key file args output Standard averaging batch process This simply calls routine average with possible given arguments The arguments for average default to 10 and 10000 start and end of the span if gt length args 2 warn batch average Too many arguments s args let start or first args 10 end or second args 10000 open diskfile file average start end save average output This batch routine is a good example what the process code should do As with all function definition the first form may be a document string
38. on to routine for creating a channel selection menu it contains also routine for defining channel sets and some utility routines that can be used from lisp code control the utility Following functions are exported clear channel selections amp optional device Clear channel selection definitions Removes all current channel defini tions for given device type If no type is defined all definitions will be cleared define channel selections devtype amp rest specs Define some channel selections Usage define channel selections devtype entry entry Each entry is a list starting with the name of the channel set followed by pick widget selection strings 10 Signal Processor channel selection 2 0 Module revision history make selection menu menu bar name accelerator pick display Make a new selection menu Make a selection menu into given menu bar This menu controls pick widget pick and display display These may be either names or widgets current selection name This variable contains the name of latest selection made Note that using this directly works only if you have only one selection menu selection default device This variable contains the default device for selection menus This can be set in the environment to choose the default set use selection device type name amp optional pick display Activate a view selection This routine sets the selection of pick widget pic
39. play the field amplitudes as a function of time Two variables are exported They contain the results of the calculation pca fields This variable is set to contain a matrix holding the field vectors pca svalues This variable is set to contain the squares of the singular values of the data matrix 16 Signal Processor Add PCA fields menu When PCA module and the SSP module are present simultaneously a menu button Add PCA fields is added to the Actions menu of the SSP dialog See ssp on page 18 This button opens a submenu that contains buttons to add 1 2 3 5 8 or 12 first singular fields into the vector pool of the SSP dialog 17 1 5 SSP ssp General Description Installing the module The package ssp provides a handy interface for managing vectors for a suppressor widget Its basic purpose is to make easy to project away exter nal disturbances from measured signal It can be used for any other pro jecting problem as well Vectors can be easily assembled both into a suppressor widget so that requested space can be removed and into a lin ear widget to show the time dependence of each vector providing effec tively a linear multi source model The subspace that we are interested in is defined by a set of vectors or matrices These vectors define the subspace that they span Vectors need not to be orthogonal and can have arbitrary length The lengths have no effect in pro
40. root batch states The name of the batch file should be name 1sp where name is the name of the batch A batch may have same name as some previously defined function since the batch names are kept in a separate name space Syntax of a state description is as follows define batch states state definition name base setup name modification modification Where the state definition name should be a symbol that matches the name of the file where the definition is saved The base setup name should be a string defining a Graph setup file name compatible with LISP function load settings If the state file is available in your personal setup file directory the base name of the setup is enough for example basic If not complete file path is needed Extension can be left out if it is setup Signal Processor batch processor 1 4 Modification entries describe how the signal processor state created by the setup routine should be modified to reach a specific processing state The modifications can have two possible forms First lt simple modification gt name extensions lt lispform gt lt lisp form gt The lt name extension gt is a string to be appended to the file name of the output file when this modification is applied to the base setup This term is always needed The rest of the definition is a sequence of lisp forms com mands that are evaluated to modify the base setup
41. selections vv Standard channel selections for Elekta Neuromag templates This is a utility that manages a template filter to ease template matching operations trigger utils Set of utilities to ease trigger and event handling xfit Utility that enables easy transfer of data from Graph to Xfit xplotter Utility that enables easy data transfer from Graph to Xplotter ROO Changes to the reference The reference has been updated for Graph version 2 94 Batch processor interface images updated to correspond latest appearance Added reference pages classify by table Added reference pages for trigger utils Ssp module now adds channel names to the saved files Xfit has channel selection controls Xplotter has possibility to overlay data Added module version history to several modules Signal Processor batch processor 1 4 1 1 BATCH PROCESSOR 1 4 General Description Installing the module Components of a batch definition Batch processor is a module that enables you to apply predefined process ing to multiple data files It essentially takes a list of files and processes them to produce some output files It provides an easy to use window based interface to define the files and processing to be applied in addition to built in name generation for the output files Processing definitions allow also multiple runs on each file with the data processing system tuned to slightly different settings These routines also crea
42. splays See Selecting time intervals in Signal Processor User s Guide Activating this button will transfer data in widget defined by the user variable default data source within the selected time span to the Xplotter program It also performs an autoscale opera tion Kill xplotter Activating this button will stop the slave Xplotter program used to view data by this menu In addition to the xplotter menu this module exports several functions that are useful in operating with Xplotters This module is for example needed by the command widgets created by the Xplotter button in the Widgets menu Here is a list of functions and parameters currently pro vided For detailed information on the functions use on line descriptions of the functions e kill xplotter Function that stops a Xplotter process 38 Signal Processor xplotter 1 2 Module revision history e xplotter Function that starts a xplotter process Variable that contains the stream used in communication with the Xplotter used in menus e xplotter command Function that sends a command to a Xplotter e xplotter load Function that loads a file into a Xplotter Both replac ing the existing data and overlay are supported e xplotter menu Function that creates the xplotter menu Variable containing the xplotter menu e xplotter program Variable containing the start up command used to start a Xplotter process xplotter show data Function th
43. t is found this classifier function is called with the trigger time and the return value is used to tag the epoch The average widgets contain a field tag which defines the event tag to which it responds If the tag does not match no averaging is performed So by writing a suitable classifier one can easily average epochs belonging to some particular class The tag can be any LISP object but using strings is preferred 12 Signal Processor classify by table 1 2 What classify by table does The operation of the routine is defined by a table file which is a Lisp file having fixed structure The file contains a list of definitions one for each class These definitions contain the tag and information that is used to define the class When the routine is called it examines the trigger channels for a trigger combination In order to make this work the setup must contain a channel which carries the combination information In systems that do not provide binary coded trigger combination channels dacq 3 3 and earlier easiest way to create such a channel is to use encode widget Syntax of the event tag table The following paragraphs describe the format of the table It is actually read indirectly as a lisp object so it resembles a function definition The file should contain one list starting with symbol event tag table That should be followed by the entries which also are lists The first element of the entry defin
44. tails how the fit is actually done depend on settings of the Xfit program The length of the data transferred is defined by user variable xfit region width that is available also through Parameters menu button Misc defaults If the selected point is within data that is currently transferred into Xfit no data is transferred only a fitting is performed Kill xfit Activating this button will stop the slave Xfit program In addition to the xfit menu this module exports several functions that are u seful in operating with Xfit Here is a list of functions and parameters currently provided For detailed information on the functions use the on line descriptions of the functions kill xfit Function that stops the Xfit process xfit Function that starts a xfit process Variable that contains the stream used in communication with the Xfit used in menus xfit command Function that sends a command to a Xfit xfit fit selected point Function that fits current selected time point using Xfit See menu button Fit selected point above xfit fit span Function that makes multiple single dipole fits over the defined time span Channels used in fits can also be selected xfit load Function that loads a file into a Xfit xfit menu Function that creates the xfit menu Variable containing the xfit menu xfit region width Variable defining the length of the data trans ferred into Xfit when functions xfit pick selected point and xfit
45. te a log file that records proceeding of the batch processes and possible error and log mes sages delivered The batch processor module is supplied with the Graph version 2 92 and later in the standard module library neuro lisp graph lt version gt lib and to load the code into the system you need to give lisp command require batch processor After this command the functionality of the module should be available Note however that the setup files that are used to save Graph state are capable to load the code automatically if the module was present when the setup was made Is such case loading the setup will load the batch proces sor automatically A complete definition of a batch process consists of four parts e 1 List of files to be processed possibly with some extra arguments e 2 Output directory 3 A set of signal processor state definitions 4 A description of process to be applied The file list is simply a list of file names However there can be a set of arbitrary extra arguments attached to each file Same file can not be entered twice with same arguments The arguments are passed to the pro cess code and they are process dependent and documented elsewhere for each process Output directory is the name of the directory where the output files should be saved One can use special value source to denote that the output files should be placed in the same directory where the corresponding source file is
46. the ssp vec tors but the title on top of the box changes from SSP vectors ON to SSP vectors OFF to show that the vectors are not used just now To acti vate the vectors again press the On button The File menu contains commands that are related to saving and loading projections In addition it contains the Close button which closes the dia log The Edit menu contains commands that are related to manipulating the projections and the Actions menu contains mainly commands that are used to create new vectors Note that other modules may add buttons into this menu These additions are not documented here See for example pca on page 16 Following paragraphs describe what each menu button does Default directory To set the default directory for the projection files use menu button Default directory in the File menu This pops up a file selection box for easy setting of the directory The directory is defined by user vari able ssp default directory so that the value is saved into setup files and you can alter the value also using lisp commands Save To save selected or all if nothing is selected pool vectors use the Save button in the File menu This will pop up a file selection box and you should enter into in the file name where you wish to save the vec tors The file name must have either extension Isp The extension is used to decide in which format the files are saved Nor mally it is b
47. they should be created by a suit able setup This module is available in standard module library of Graph so that you can load it by command require ssp Note that setup files are also capable to load this module so that if your current setup provides the module you don t need to enter the command 18 Signal Processor ssp Using ssp dialog Activating vectors When the module is loaded it creates button SSP dialog in the Com mands menu Selecting this menu button will pop up a dialog for projec tion manipulation To close the dialog use menu button Close in the File menu of the SSP dialog A picture of the dialog is shown below SSP vectors File Edit Actions Vector pool E SSP vectors ON Blink1 122 1 Blink1 122 1 gt proj_item_001 122 1 On top of the dialog there is a menu bar that allows user do execute some commands Below the menu bar are two selection boxes with some but tons in between The left box the Vector pool lists a set of space defini tions that can be easily used in the operations but which are not active that is being used to define the subspace used On the right side in the SSP vectors are represented the definitions that are currently being used Each space definition has a name The text in the selection boxes state the names and sizes of the matrices that define a subspace Note that the length of the d
48. troduction isset eese es boe bete 1 Changes to the reference sss 2 batch processor L 4 tan anh Pahoa teat cade or e a uote 3 General Description 3 Installing the module essere ene 3 Components of a batch definition 3 User interface sace e t hv eo a tae eee den 4 Testing batches rear einen ines 5 Running batches iive e aH eta etx uS 6 ReSIriCHOHS HE HIR Rr ORE EE ERR ER GS ERG 6 State description syntax eene 6 Process definition syntax 7 Example process definition 8 Module version history sess enne enne 9 channel selection 01 ess torneo sicnt ag ekeren eden 10 General Description 10 Installing the module eene 10 F nctionality eese de rire 10 Module revision history essent 11 Class COCA DIES ui ot Ral 12 General Description _ annannvennennvenv eene 12 Installing the module reete eet 12 Setup files provided siete eee 12 User interface uie 12 Technical details sni tete bora aee 12 Developing enne 0640660 40806604 14 DeDUS SUNG semi aes reme eie eite 15 Module revision history 15 PCA oui Rt 16 General Description
49. y are similar to ones used in the averager and they take a trigger time and return the class of the event 32 trigger utils 1 9 Signal Processor Second following functions can be used to search events from data find event Scan data until a particular kind of an event occurs Return an event object describing the event This routine has various options defining what events are included and how triggers are handled e map events Scan events in a given time span and apply a given func tion to each of the events Module contains also a set of low level functions that are used by the above described functions and may be useful in other contexts too e classify event Classifies signals at particular time moment to deduce event class of an event This relies completely on given or default clas sifier e channel exists p Check that given widget exists and that given chan nel number is within existing channels of that widget e time span available p Check that given time span is available from a given widget e signal present Check if the signal in given widget channel time span is nonzero e get stimulus combination Get data value from given default trigger channel at sample which follows given time Module revision history Changes to the module trigger utils 1 9 e Changed the calling convention in map events Modified the also the way find event behaves when no tags are defined trigger utils 1 8 e
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