WFU SPM5 PIPELINE User Manual v1.0
Contents
1. check_paradigm_lookup_table ksh IMPORTANT NOTE Autoprocessing from MoJoe a directory of dicoms or a compressed tar of dicoms will only reference these paradigm lookup numbers if dicom field 0019 10e0 is set to a reference number Otherwise a paradigm file will need to be placed in the study s root directory See section 2 2 4 Autoprocessing 4D files from the Command line for more details Running the included sample study Place the lines in the above excerpt in the WFU_PIPELINE ref_functions paradigm_lookup_table or if a paradigm_lookup_table does not exist copy the template over Then see section 2 1 Using MoJoe 1 4 Compatibility The spm5_pipeline has been tested in the following environments WFU s Pipeline Environment Testbed OS Version Solaris 9 Gentoo Linux 2008 0 Red Hat Enterprise Linux 4 amp 5 GCC Version Solaris 3 4 2 4 1 2 RHEL 3 4 6 and 4 1 2 Sun Grid Engine 6 0u8 6 2 Matlab Version 7 3 0 298 Matlab 2006b 7 3 0 298 Matlab 2006b The spm5_pipeline should run on most linux platforms without modification The pipeline should run on UNIX Solaris without modification although MoJoe may not be able to be built against it MoJoe currently runs on GE LX MRI Scanners 15 WFU SPM5 Pipeline v1 0 maldjian wfubmce edu 1 5 Referencing the software 2 Using the Software 2 1 Using MoJoe Mojoe can be called from the command line at the scanner console with cd2. 926 2325113 262 374 208 634255 PAN 5 Gly Ao Alsiishy7 GUO 5 Sieye i straight timing setup any paradigm se Ne Ne oN Ne Ne Ne Ne PNFPOFPOrRPOFRSO s End 40 10 31 il 30 il 40 i 50 600 WFU SPM5 Pipeline v1 0 maldjian wfubmc edu Once a reference function is written it must be linked with its paradigm lookup number This unique floating point id followed by the full path to the reference function is located in the tab delimited WFU_PIPELINE ref_functions paradigm_lookup_table Like reference functions comments may be placed in the file by prefixing the line with semi colons 14 WFU SPM5 Pipeline v1 0 maldjian wfubmc edu Excerpt from WFU_PIPELINE ref_functions paradigm_lookup_table template t 7 POEM ti 1800 home bwagner spm5_pipeline ref_functions AMP DSSTblock_1800 se_ref 1801 home bwagner spm5_pipeline ref_functions AMP DSST_Hard_1801 se_ref 1802 hnome bwagner spm5_pipeline ref_functions AMP DSST_Hard_1802 se_ref 1803 home bwagner spm5_pipeline ref_functions AMP DSST_Hard_fixedeffects se_ref As the list of paradigm number and associated reference functions can grow to be quite large and it is essential that the reference function file exist a simple check function can be run to check for the existence of the reference function file It does not check the contents of the reference function for validity cd WFU_PIPELINE ref_functions
3. from the point of acquisition This pipeline was developed in the ANSIR Laboratory at the Wake Forest University School of Medicine Questions can be referred to maldjian wfubmc edu 1 2 Downloading the Software The WFU SPM5 Pipeline can be obtained at www ansir wfubmc edu 1 3 Program Installation 1 3 1 System Requirements ksh Korn Shell Script csh or tesh C Shell Script mailx Sun Grid Engine 5 or 6 Offis s Dicom Toolkit dcmtk 3 5 4 included needs to be compiled Fast Light Toolkit fltk 1 1 2 included needs to be compiled Cdtools 1 10 included may need to be compiled FTP and SSH server installed on at least one grid node 1 3 2 Setting up the directories The WFU SPM5S Pipeline is designed for a grid computing environment It is strongly recommended that pipeline files be placed on a filesystem that is accessible to all computers that are on the grid While it could be individually installed on each grid computer this is not recommended Data has to be stored on a filesystem that is accessible to all nodes in the grid Change to the parent directory of where the pipeline is to be installed Place the downloaded tar gz file in this directory Uncompress and extract the files in the archive tar xzvf WFU_ Pipeline tar gz WFU SPM5 Pipeline v1 0 maldjian wfubmce edu The following directories and many further subdirectories will be created WFU_Pipeline The root directory of the pipeline WFU_Pipelin
4. 11 1 3 10 Final installation and setup of Mojoe if MoJoe is to be installed oo eee 11 1 3 11 Refer nce FUNCIONS seisis teso aa aaas aR aaa a aaa aaie 12 LA Compatibility sisca a EE A E E eee 15 LS Referencing the SOMWALG f csccpcievssnepeevacnedadaaavsdacsvansosaianedcasusaadedaaswodadsiapsedesasubecdsasgoadasaeedass 16 2 MBAS th OT A ao ese ts eo ta oar educa ey de adtse a ea ai a ees taadad lead eae ES t 16 2 Usine MOJOE acca tastes caches aes cap eet ees eee te ee a eee Gece ER 16 2 MoJe CBU snr aaa a aeaa aai 16 22 MoJo EX aC tsiere edegi eie a rE e TEA AET n Eas eSis 17 2 2 FAMMOPEOC ES SUNS inosia icient ana a Kaa aa aE E EE eee AaS E STES 18 2 2 1 Autoprocessing from MoJoe esessseseesessersseeressessrrrresserstesesstesteseresteseesreesteseeeereseenee 18 2 2 2 Autoprocessing P files from the Command line esseeeeeeeeeeeeseesreeseeressersrerrersreereeseese 18 2 2 3 Autoprocessing DICOM images from the Command line DICOM images that do not have the paradigm number set acco ete cpesceece Se sencans a dete seczansneuuceeseepuenteenctaltcoonenuorecaecngenqeutiae 18 2 2 4 Autoprocessing DICOM images from the Command line DICOM images that have the paradim number SOU secede ieascniostussecasenndecesc eda aar e ERE ar aaa EESE iTi 19 2 2 4 Autoprocessing 4D files from the Command line sseesseeeeeseseeesreesesrrssreeresressreeresresse 19 2 3 Reprocessing and Error Recovery sisisescacssciasscecianievessaseasnasadbavenda
5. If this method followed the WFU SPM5 Pipeline user s will have to have this directory added to their path Note the MoJoe compiling script will expect DCMTK to be located spm5_pipeline dcmtk 3 5 4 WFU SPM5 Pipeline v1 0 maldjian wfubmce edu Uncompress and extract the files in the dcmtk archive cd WFU_PIPELINE tar xzvf external dcmtk 3 5 4 tar gz Configure the package to your system This documentation will refer to an install in the opt directory To use the standard linux bin directories remove the prefix opt option cd dcmtk 3 5 4 configure prefix opt Next make the DCMTK package and install it Do not run make clean if planning to use ModJoe make make install Note DCMTK may now need to be added to your path If which demdump does not find the command then this must be done 1 3 4 Configuring the SPMS Pipeline Depending on the default shell for your users several files will need to be created modified for the WFU SPM5S Pipeline to run On our test system with the default shell being bash the following are required files and the appropriate settings bashre file The default shell etc skel bashre This file is sourced by all interactive bash shells on startup including some apparently interactive shells such as scp and rcp that can t tolerate any output So make sure this doesn t display anything or bad things will happen opt sge6 default common settings sh for dcemtk ex
6. README References Maldjian JA Baer AH Kraft RA Laurienti PJ Burdette JH Fully automated processing of fMRI data in SPM from MRI scanner to PACS Neuroinformatics 2009 22
7. shades tiasacaetastecedsannapassioncncs 20 DU MG ANE UM eases iei n a EE E A A e EE aAa 20 2 3 2 TETUN aiarren N E E E E E O N 20 233 Tern LOCAL 2icessicveckintelesisavecccestacedasesbecedessiebussasbeacecstacedacael 20 2 34 duek sta tasien ea a a a a r E aE E S 20 3 Technical NOteS rsscisecoioaron iieri i een EE EE NEET RTR 21 3 1 Transfering of fMRI analysis to PACS wcssiccnscsnczercseservssceceseosanceedacyseansnaceancacscusseadgoceuatesies 21 3 2 WRU Grid Distribution Tool ecaceeencuscceutusdenedeuaddvapsuuedcauvdadacs ds ctaaavandadanpeluneaduiydademenabeacesucadaes 21 ReferentEg seisis aiei eiea ina EEE EA EAA EE EEEa EES EETA Eaa ia aiea 22 WFU SPM5 Pipeline v1 0 maldjian wfubmce edu WFU SPM5 Pipeline version 1 0 User Manual Joseph Maldjian MD 1 Software Description Installation and Setup 1 1 Description The WFU SPM5 Pipeline is a fully automated method for the processing of fMRI data using SPM It is fully automated from the point of data acquisition at the MRI scanner It incorporates tools for automated data transfer archiving real time SPM5 batch script generation with distributed grid processing automated error recovery procedures full data provenance email notifications optional conversion back to DICOM Digital Imaging and Communications in Medicine and picture archiving and communications systems PACS insertion The architecture allows for an infinite number of easily definable analyses that are fully automated
8. 6 images 42 events ti use 1 to indicate baseline in this case trials with only 1 matching probe number 70 indicates null images ie not to go into analysis note that baseline should now be considered a VIGO MGbeteatOny ae DUCEAU NERO t SMO Use the to end long lines to continue into next line names lists the conditions in numerical order paradigm_name email cE conditions images ER fixed mixed names contrast_names contrast _types contrast_values DSST_Hard_1801 bwagner wfubmc edu cue prolmatch pro2match pro3match Gte act Prol ace Dro act e AOS Gicle Apro Eo rEpro 2 jereoill_wicie joes S pro sgt ripro oe lL_jieie EPOS T T 1 0 0 0 0 1 0 0 0 0 1 0 Or 0O ly Or e Or lOr ip OS O0 ii 00N fixed_effects_paradigm_name Fixed_effects_lookup_code dispersion_derivative DSST_Hard_fixedeffects 1803 0 time_derivative time_derivative_weight dispersion_derivative_weight processing_type high_pass_filter low_pass_filter auto_correlation eS ee onl rer begin condition appears in the first column time in seconds appears in the second column The comma separator must be used to separate fields this format can be used for single event pseudo random experiments to check if the format is valid use the function read_seref make sure conditions above match number of conditions below note that baseline is now considered a condition ONLY USE 0 FO
9. R NULL IMAGES ie to be discarded r blocked paradigm setup no ER flag ii Plollioelke Br doy Pope dha Bind poe dig Oop Ab time 7 42 9 ToLOcksa Ip Bo ler Op dp BelpApOn tp Sele Sr Opi 2 lye 0 8 7 IO N T aa time 5 Bp Sp Bp Dp 207 Dp Sy Dp De 20 7 Bp Sp Dp Bp 20 Sp Sp Sp S720 8 8 87 Bip Bp Sip 207 Dp Op 9p Bp 20 Bp Op Sp Op BO Bp Sp Sp Op ZO t fixed event setup ER flag and fixed flag gal pisi T i2 sisi r 14 10 30 variable event setup ER flag no fixed flag 1 r 2 r 3 r 4 r 1 0367 6 923 135 119 LS 225 0657S SOA Sh OO OO IE SS ST Gl 407 617 893 13655 19 5928 85 44775 Ml S74 97 Ave LOS SGL LOL WILLS eae W2 tals t327 2i 242 MSs LAs OOS TIS 8587 139 364 A5 SEGS 963 USS Os 164 LVS LIO 1S 176 063 AAS eS Br Shi pL IAT oA OF AO Ol 495722 Ol Oo Sins Vip ALE 5 1B 224 n VIG 2305 VL S37 236 BST 1966724972549757 260079747 Ao SaaS BUS 5 SUSE WS 2D ONS ZES O 220 sets 297 6067 084 308 969 315 DAO AO cA GZ BOV LOL Kil Taso ISS S 135 258 159 Alen 171 Se 1S 628 Lo TL TE AV sO 2A0 IA 2c AGI BAG ASG 20 S 274 443 280 478 14 S12 20 52 SoS 565 907 74 9574 2 ITA MSI LL 17S L29 403 153538378 16S VIS SOd reS 2 1 6 GL AAs LS ACs SIS ps 298 467 304 484 316 4 Bo Seep 525904 44 S519 O05 IN OS o QES 80 932 SO i347 iy ios lal 262 LA S66 amp LY AOS 195
10. WFU SPM5 Pipeline v1 0 maldjian wfubmc edu WEU SPMS5 PIPELINE User Manual v1 0 ANSIR Laboratory Wake Forest University School of Medicine WAKE FOREST UNIVERSITY SCHOOL of MEDICINE WFU SPM5 Pipeline v1 0 maldjian wfubmc edu 1 Software Description Installation and Setup cee eee eeseceseeeeeeeeeeceaeceseeseeeesaeecsseesnaeenseesees 3 1S IRN Yas 610 cs iespiesta aao e iaa ee aE e ere 3 1 2 Downloading the Software sseeesseseeseeeseesessersesreesrtsrserssrestsrrestesstsetestenstsetsstesstestesreesetet 3 1 3 Programi Trista Va OU sisisi iari eia a EEEE A ER S 3 Led System ReguiremMentS ciiise EE EE oaenceeeles 3 1 3 2 Setting up the directories aja dis sds decetea dened cbeseukceecetidesedadedelendasdosdaiedictdaasebededeededeztadoneeeds 3 1 3 3 Compiling required component DCMTK sseessesseseesreesesressrssrrsressersrerreesrrseresresseeeees 4 1 3 4 Configuring the SPMS Pipeline neiseina 5 1 3 5 Considerations before compiling and using MOJ0e cecesceeseeeeeseeeecetececseeeeesneeeenee 7 1 3 6 Compiling optional component FLTK required for MOJ0 0 0 eeeceeeeeeeeseeeeeteeeeeee 7 1 3 7 Compiling optional component MOJ0 ee eeceeseesseceeeeeseeeeaeeceaeceaeeeseeesaeessaeeneeneees 8 1 3 8 Configuring MoJoe if MoJoe is to be installed ee eee eeeeceseeeeeeeeaeeeseeeeseeeeeeeenees 8 1 3 9 Optional Transfer of MoJoe to a MRI scanner uu ee eeeeceeeeeeeeeeeecnseeeeeeeeeeeaeesaeenes
11. aradigm or processing from dicoms Again it is recommended to run cleanrun before rerunning WFU_PIPELINE bin rerun_Icoal path to subject_directory 2 3 4 quick_start Autoprocessing creates several batch_que and batch flist files in directories such as the log batch batch RUNx and FIXED_EFFECTS directories If processing completes normally then the batch_que files should all have a file size of 0 However if an error occurs one or more of these files will still have commands that need to be executed After the error is fixed a batch_que can be continued by issuing the guick_start command found in the batch_que s directory To get a listing of all the batch_que s in a subject folder type find name batch_que xargs Is lhrt To completely restart a batch_que copy the batch flist file over the batch_que file Then edit the batch_que removing the number that might be found at the top Then the quick_start command can be issued 20 WFU SPM5 Pipeline v1 0 maldjian wfubmce edu 3 Technical Notes 3 1 Transfer of fMRI analysis to PACS The WFU SPM5 Pipeline will automatically convert an analysis to DICOM and attempt to send to a PACS server if the study s path contains the word clinical The pacs server information is stored in the file WFU_PIPELINE WF U WFU_dicom5 wfu_dicom_magilla m Matlab file To change the pacs server to which files are sent edit the lines WFU_PIPELINE WFU WFU_dicom5 wfu_dic
12. arts This should include the WFU_PATH and WFU_SPMS path The WFU_PATH and WFU_SPMS references the variables already set Finally copy the global site ksh template file to global site ksh cd WFU_PIPELINE WFU cp global site ksh template global site ksh Ata minimum edit global site ksh file and configure the following settings refdir su_email email_address rsh_flag mailserver mail_flag timekeeper batch_display batch_matlab Full path of the reference functions Super user email Place the username of this person after the grep command Change the domain name as appropriate If set to 1 then the mailserver and timekeeper may be used for specified task Otherwise the local machine will Hostname FQDN or IP of the main computer to send emails from If set to 1 then the mailserver will be used to send emails If set to 0 then the computer which runs the script will be used This is only in effect if the rsh_flag is set Hostname FQDN or IP of the computer used to get the date and time Hostname FQDN or IP of the computer to push all displays from Matlab to This computer must have an X server installed and xhost issued on it Full path to the Matlab execution script along with arguments used at startup It is recommended that the options nosplash and WFU SPM5 Pipeline v1 0 maldjian wfubmc edu nodesktop be used The nojvm option can also be used but may not be su
13. ation while the fmri and bin directories can be placed in a more restrictive read only location The billEmail and monitorEmail are email addresses that email should be sent for the person who would keep track of billing and monitoring These email settings are also affected by the assorted email settings in spm5_pipeline WFU global site ksh The billRemoteDir and monitorRemoteDir are remote directories used to store mojoe session information Note Even if not being used the monitorRemoteDir and billRemoteDir must exist The last section starting with PIPELINE_DIR and the assorted MOJOE_ settings depend on the location of MoJoe If MoJoe is being used in a sample testing environment then the PIPELINE_DIR should be the location of the spm5_pipeline directory However on a scanner MoJoe should be installed in a mojoe directory under the home directory of the user and all these settings should be commented out with a as the first character on the various lines If MoJoe has difficulty finding data on the scanner this section is available to specify the location of the assorted directories 1 3 9 Optional Transfer of MoJoe to a MRI scanner To transfer MoJoe to a MRI scanner first tar and optionally compress the mojoe directory Then move the tar file to the scanner and extract it On a scanner mojoe should reside in the mojoe directory Edit the settings ksh file for specific settings of the scanner being used Sample comman
14. ds from the spm5_pipeline directory one the computer which MoJoe was compiled tar czvf mojoe tgz mojoe transfer mojoe tgz to the scanner place in home directory cd tar xzvf mojoe tgz 1 3 10 Final installation and setup of Mojoe if MoJoe is to be installed Note This series of commands will have to be run from each scanner computer on which MoJoe is installed MoJoe uses SSH keys in the transfer of data from the scanner to the computing grid On the scanner or sample computer if ssh id_rsa pub already exist please skip to the third line In the commands below replace sshuser and sshserver with the respective settings from settings ksh SCANNER NAME should be the name of the scanner computer which these commands are running on 11 WFU SPM5 Pipeline v1 0 maldjian wfubmce edu cd ssh keygen t rsa choose the default options with the suggestion of leaving the passphrases blank scp ssh id_rsa pub sshuser sshserver ssh id_SCANNER_NAME pub ssh sshserver log in as sshuser cd ssh cat id_SCANNER_NAME pub gt gt authorized_keys While on the scanner create the directory export home1 mojoe or the directory specified by MOJOE_TEMP in settings ksh mkdir export home1 mojoe Change to the mojoe directory and run the goMoJoeSetup command Follow the onscreen instructions cd mojoe goMoJoeSetup Note If using on a sample computer choosing ESE 14 will allow you to the sample pfile script spm5_p
15. e WFU Mainly Matlab code used in autoprocessing WFU_Pipeline bin Scripts useful for processing WFU_Pipeline doc Documentation WFU_Pipeline external Source code for needed libraries WFU_Pipeline fmri Scripts used in autoprocessing WFU_Pipeline mojoe source code for MoJoe WFU_Pipeline ref_functions the location of assorted reference functions and setting for MoJoe If the sample_data has been downloaded place it in the same location as the WFU_SPM5_Pipeline tar gz and uncompress it as well tar xzvf WFU_Pipeline_Sample_Data tar gz The following directories will be created WFU_Pipeline poem052_08_28_08 A sample study WFU_Pipeline testbed a sample MRT directory structure for testing MoJoe Next set the environmental variable WFU_PIPELINE This will depend on you default shell For a bash type shell cd WFU_Pipeline export WFU_PIPELINE pwd For a csh type shell cd WFU_Pipeline setenv WFU_PIPELINE pwd Note The tick marks above are back ticks found usually above the tilde key To check that the variable has been set correctly printenv grep WFU_PIPELINE 1 3 3 Compiling required component DCMTK The WFU SPMS Pipeline requires access to several executables found in Offis s Dicom Toolkit http dicom offis de demtk DCMTK may be compiled installed as root and placed in one of the standard bin directories Alternatively it may be compiled installed as an unprivileged user and placed in alternative directory
16. eate a directory in the study root called nifti and place the structural image in this directory WFU_PIPELINE bin wfu_ AUTOSPM5 full path to study_directory 19 WFU SPM5 Pipeline v1 0 maldjian wfubmce edu 2 3 Reprocessing and Error Recovery 2 3 1 cleanrun The spm5_pipeline bin cleanrun command will clean out a subject directory removing all processing data and assorted file lists flists ques etc It will leave the locs DICOM archive p files and user created directories Several files will also be deleted from the log directory If a subject is to be reprocessed it is recommended that this command be run first This script will not restart processing WFU_PIPELINE bin cleanrun path to subject_directory 2 3 2 rerun The spm5_pipeline bin rerun command will reprocess a study starting with DICOM conversion Before reprocessing several files and directories are deleted then the reprocessing is placed on the grid This command will work only if data came from a MoJoe extract manually using autolocsort_excite_paradigm or processing from dicoms It is recommended to run cleanrun before rerunning WFU_PIPELINE bin rerun path to subject_directory 2 3 3 rerun_local The spm5_pipeline bin rerun_local is the same command as above but the initial DICOM conversions will be run on the computer which the command was issued from This command will work only if data came from a MoJoe extract manually using autolocsort_excite_p
17. equires dicom conversion 4D image creation creating a file paradigm pair text file and then autoprocessing Given a study directory and within that directory a directory of dicom images called dicom_images the following command would be called WFU_PIPELINE bin wfu_CONVERT_DICOM study_directory dicom_images Create the processing paradigms textfile see below WFU_PIPELINE bin wfu_AUTOSPM5 full path to study_directory The wfu_CONVERT_DICOM command will create several 4D files in the study s root directory These then must be linked to the appropriate paradigm number in a paradigms file The name before the paradigms does not matter but there may only be on paradigms file in the study s root directory Waiting until after the wfu_CONVERT_DICOM step for generation of this file is due to the unique structure of the 4D file names subjected series number slice number number of images PSD name _4D img hdr A sample processing paradigms file for the included study is given below Sample processing paradigms POEM052 0006 267 0001 9345 epiflexfmri_4D img 1800 POEM052 0007 170 0001 5950 epiflexfmri_4D img 1801 POEM052 0008 170 0001 5950 epiflexfmri_4D img 1802 18 WFU SPM5 Pipeline v1 0 maldjian wfubmc edu 2 2 4 Autoprocessing DICOM images from the Command line DICOM images that have the paradigm number set Autoprocessing of DICOM files can occur in two ways with either a tar gz of DICOMs or a directory of DICOM
18. fore using mojoe For example the above referenced user should have the following directories already created studies2 bwagner test1 studies2 bwagner test2 and studies bwagner test3 The only file in WFU_PIPELINE mojoe to configure is the settings ksh template file First copy the template to settings ksh cd WFU_PIPELINE mojoe cp settings ksh template settings ksh WFU SPM5 Pipeline v1 0 maldjian wfubmc edu Mojoe settings ksh sshserver elfido medeng wfubmc edu sshservername S sshserver can be used to shorten the server or a alpha name if the above is an IP sshuser mojoe_ssh sshpass junk2007 this is the location of the reference functions directory on the FTP SSH server ref_dir home bwagner spm5_pipeline ref_functions these are the locations of assorted directories in the pipeline fmri_dir home bwagner spm5_pipeline fmri bin_dir home bwagner spm5_pipeline bin billing info billEmail bwagner wfubmc edu billRemoteDir studies mojoe_bill monitoring info monitorEmail bwagner wfubmc edu monitorRemoteDir studies mojoe_monitor this is the location of this mojoe installation on a test box on a scanner this should be in a directory called mojoe off the user directory and all lines below should be commented out PIPELINE_DIR
19. hen a sample capture can be done by opening two terminal windows In one start mojoe Initiate the capture routine Then in the other window cd WFU_PIPELINE testbed newCapture ksh 16 WFU SPMS Pipeline v1 0 maldjian wfubmce edu After a few waiting 15 lines press Ctrl C to break the script MoJoe will then finish the capture Note The p files included in this sample script are for ESE14 If using a different version change the last line of the script to the appropriate version 2 1 2 MoJoe Extract When the Extract button is selected a pull down menu and selectors will appear for selecting the series to be transferred Once selected the images are extracted from the scanner database assembled into a compressed tar file ftp d to the specified disk and then burned to CD gt lt Extract v3 14 bwagner SubDir testi Subject subjecti 2473 08 28 2008 11 08 31 POEMOSZ 1 3 Plane_Loc 15 5 Obl_Ax 3D_SPGR_S2 124 6 fMRI_dsst_1800 9345 7 8 fMRI_hard_1_1801 5950 fMRI_hard_2_1802 5950 F Check All Start Cancel Figure 2 MoJoe Extract Widget The extract widget provides pull down menu listing exam number and subject names for data in the scanner database Exam Subject label subject1 is used to label data during transfer and archival Selected series to be transferred can be checked off in the check boxes within the list of series If MoJoe is being run on a test computer
20. home bwagner spm5_pipeline OJOE_DIR SPIPELINE_DIR mojoe OJOE_POOL PIPELINE_DIR testbed imagepool OJOE_TEMP SPIPELINE_DIR testbed temp OJOE_CONFIG SPIPELINE_DIR testbed config OJOE_SERVICE SPIPELINE_DIR testbed servicelog OJOE_DATDIR1 SPIPELINE_ DIR testbed datdirl OJOE_DATDIR2 SPIPELINE DIR testbed datdir2 OJOE_WHATREV S PIPELINE_DIR testbed Rev OJOE_PROTOCOLS_TOP SPIPELINE_DIR testbed OJOE_RAW SPIPELINE_DIR testbed raw OJOE_GRAVEYARD SPIPELINE_DIR testbed graveyard OJOE_GATING S PIPELINE_DIR testbed gating ONLY CHANGE THESE IF YOU _MUST_ HAVE A DIFFERENT USER PASS FOR FTP ftpserver sshserver ftpservername S sshservername ftpuser S sshuser ftppass sshpass The above code is the pertinent configuration settings in mojoe settings ksh The first section deals with the SSH and FTP user that MoJoe uses to communicate from the scanner to the grid If SSH and FTP need to be different users please edit the appropriate section further down Future versions of MoJoe should make this section unnecessary ref_dir fmri_dir and bin_dir are the full path names to the spm5_pipeline ref_functions spm5_pipeline fmri and spm5_pipeline bin directories respectively On our installations these directories are not all under the spm5_pipeline directory 10 WFU SPM5 Pipeline v1 0 maldjian wfubmc edu For example the reference functions directory may need to be in a read write accessible loc
21. images under the study s root directory WFU_PIPELINE bin wfu_LFULLPROCESS path to study_directory study tar gz or WFU_PIPELINE bin wfu_FULLPROCESS path to study_directory dicom_images The sample study can be run by typing as one line WFU_PIPELINE bin wfu_FULLPROCESS WFU_PIPELINE poem052_08 28 08 poem052_08 28 08 3235 tmp tar gz If creating a tar file for processing without the assistance of MoJoe it is recommended that you follow this form for the tar file structure The autolocsort_excite_paradigm script will expect the archive to be based on a tmp directory The directory structure afterwards may be based on preference Sample Directory Structure of a DICOM tar gz Archive from MoJoe tmp 02473 exam number 0001 series number OOL cien image O00 Ca image ete 0005 series number OOM dem image W002 Cen image Ete 0006 series number OOO Cem image O00 Can image ete Note Exam series and images may be named differently For example e2473 s1 IO1 MRDC 1 respectively 2 2 4 Autoprocessing 4D files from the Command line If 4D analyze or nifti data files already exist in a study directory along with a structural image then autoprocessing can be completed by Creating a processing paradigms file See section 2 2 3 Autoprocessing DICOM images from the Command line DICOM images that _do not have the paradigm number set for details creating this file Cr
22. ipeline testbed newCapture ksh Otherwise that file will have to be modified for the specified ESE version Lastly CDRECORD should be installed on the scanner in order to burn CD s Cdrtools http cdrecord berlios de is used to burn CD s As these utilities often require root privileges a compressed tar of the applicable files has been placed in the mojoe directory called linux_cdrecordsrc tar gz This file will fill the mojoe CDRECORD directory From the mojoe directory as a root user tar xzvf linux_cdrecordsrc tar gz Note If the files included in the tar do no work with the system the original source is available in the spm5_pipeline external directory Please read the documentation included with the package for installation instructions 1 3 11 Reference Functions Autoprocessing requires a paradigm reference number assigned to specific reference function file The reference function is a text based file containing a header defining the TR number of images number of conditions type of paradigm desired contrast comparisons and types and the actual paradigm definition indicated by begin and end A detailed paradigm used for the optional sample study is given on the next two pages Comments may be placed in the file by prefixing the comment line with a semi colon 12 WFU SPM5 Pipeline v1 0 maldjian wfubmce edu WFU_PIPELINE ref_functions AMP DSST_Hard_1801 se_ref This is the Hard DSST event related paradigm 17
23. ith MoJoe is not the most recent it is recommended to compile FTLK in its source directory and not install it to the system directories Note The MoJoe compiling script will expect FLTK to be in located spm5_pipeline fltk 1 1 2 Uncompress and extract the files in the fltk archive cd WFU_PIPELINE tar xzvf external fltk 1 1 2 source tar gz Configure the package to your system cd fltk 1 1 2 configure prefix WFU_PIPELINE fltk 1 1 2 WFU SPM5 Pipeline v1 0 maldjian wfubmce edu Make the FLTK package Do not run make install or make clean from the fltk 1 1 2 directory make cd FL make install 1 3 7 Compiling optional component MoJoe MoJoe has several executables in the mojoe directory that need to be built To ease this process a Korn Shell Script has been written to compile all the needed parts cd WFU_PIPELINE mojoe makeall_mojoe 1 3 8 Configuring MoJoe if MoJoe is to be installed MoJoe has several configuration files found in two locations WFU_PIPELINE ref_functions mojoe_users generic and WFU_PIPELINE mojoe The first directory contains information on the computing grid The second contains scanner settings and how to communicate with the grid The following files tell mojoe how your grid is set up and are found in the WFU_PIPELINE ref_functions mojoe_users generic directory disks txt Locations of assorted drives that MoJoe may send to disks2 txt Same as above but with a Wind
24. links to the data for Windows users WFU_PIPELINE ref_functions mojoe_users generic userlist username email enableitem enablesub subdirl subdir2 subdir3 clinical maldjian wfubmc edu 1 1 pasl dti fmri misc qa qa acr ee es 7 0 bwagner bwagner wfubmc edu 1 1 test1 test2 test3 The userlist file contains a list of users some settings and the studies that the users have permission to write to There should be no space in between the comma delimited settings It is recommended that the username be the PI for the study as directory that the data will be written to will be in the form of drive username study The second line is a separator to differentiate the clinical user from the research users below it WFU_PIPELINE ref_functions mojoe_users generic userdisk txt username defaultdisk bwagner local bwagner testl local2 bwagner test2 local2 The userdisk txt file defines which drives data for a particular user will be stored on The format is username study drive The username is the same as found in the userlist file as is the optional study The default disk should reference a label in the disk txt file In the above sample all user bwagner s data will go to the local disk except for those in the test1 and test2 studies Data for testl and test2 will go to the local2 disk Note The disk username directory must exist and have permissions set so that the sshuser see below can write to these directories be
25. mojoe goMoJoe MoJoe will provide a list of examinations in the scanner database and selectors for CD archival and FTP to a remote directory X MoJoe v3 1d DER Disa bwagner eI 01 e Bilal testi PatName Vv ieee SRM local Capture Extract Figure 1 MoJoe MoJoe startup widget provides pull down menu for specifying the Directory generally the Investigator SubDir study and PatName subject This information will be stored on the specifed Disk The Capture button initiates fMRI archival monitoring and transfer of RAW p file data The Extract button is used for transferring images from the scanner database FTP archival and CD burning can be turned on or off IMPORTANT NOTE When capturing autoprocessing will stop after dicom conversion and 4D image creation if dicom field 0019 10e0 is not set to a valid reference function The method of setting this field varies by scanner and scanner usage policies 2 1 1 MoJoe Capture When the Capture button is selected MoJoe will automatically monitor for any new raw data files When a raw data file is detected it is renamed with the subject label given a time date stamp and ftp d to the specified disk The file is then burned to a CD at the scanner console while scanning continues When the burn is complete the raw data file is removed from the scanner hard drive and the program continues to monitor for additional raw data acquisitions If MoJoe is being run on a test computer t
26. om_magilla m excerpt def_flags send pacs_host KENNY detmrlagsmsendmpdeSalosicmel ol a fey Oe def_flags send pacs_port 4006 def_flags send pacs_aetitle FMRI a flag def_flags send pacs_dbdir MRAW amp c flag To change the default directory of the trigger for automatic conversion to DICOM and sending to pacs edit WFU_PIPELINE WF U WFU_batch wfu_X_scriptwrite m For a GUI interface to dicom conversion and sending to PACS and additional features please download our WFU_DICOM tk This toolbox is for the reverse conversion of Analyze or NIfTI images to DICOM and for inserting the converted DICOM images into a PACS database This is very useful for clinical implementations in which it is necessary to have post processed images available for system wide review The WFU DICOM toolbox also provides routines for coregistering SPM processed and normalized fMRI t maps back to native anatomical MRI space using inverse transformation matrices and generating fused functional anatomic images based on user definable thresholds If a DICOM header exists for the native space anatomic image this information is used in converting the fused images to DICOM format This allows the post processed images to be linked with the patient s conventional MR data and retrieved as part of the same study on any PACS station during review The studies maintain all subject identifiers and retain all cross referencing capabilities If a DICOM heade
27. ows mapping column userdisk txt Defines which drives user s studies should default to userlist A list of users and the studies that they are associated with When the MoJoe setup script is run these files are transferred to the scanner Additionally the userlist file is updated each time MoJoe is run MoJoe also has setting specific to the computer scanner it is running on in the settings ksh file of the mojoe directory The settings found in these assorted files are detailed below WFU_PIPELINE ref_functions mojoe_users generic disks txt disk mount_point Mostmcansik local studies elfido studies local2 studies2 elfido studies2 WFU_PIPELINE ref_functions mojoe_users generic disks2 txt disk mount_point host_disk pc_mount local studies elfido studies elfido studies local2 studies2 elfido studies2 elfido studies2 The disks txt and disks2 txt should be nearly identical with the latter containing an extra column These are multiple space or tab delimited files The first column is the label that MoJoe will display to the user as the drive the data will be sent to The second column is the mount point to which node computer will find this drive The third column is the NFS mounting WFU SPM5 Pipeline v1 0 maldjian wfubmc edu information MoJoe needs in order to data The fourth column disk2 txt only is the Windows share name for the disk location This is so that the emails sent out automatically can have
28. port DCMDICTPATH opt lib dicom dic opt lib private dic For spm5_pipeline This should go before the interactive shell test exits export HOST S hostname export WFU_PIPELINE home bwagner spm5_pipeline export WFU_PATH WFU_PIPELINE WFU export WFU_SPM5 home bwagner spm5 export MATLABPATH WFU_PATH WFU_SPM5 Test for an interactive shell There is no need to set anything u pase thils Dolne 0L S09 anc 209 nE stltn Suelimp omni Co Terrein Eio outputting anything in those cases ae IL S I sae JI p then Shell is non interactive Be done now return fa WFU SPM5 Pipeline v1 0 maldjian wfubmc edu cshrc file Default shell for SGE source opt sge6 default common settings csh for demtk setenv DCMDICTPATH opt lib dicom dic opt lib private dic For spm5_pipeline This should go before th interactive shell test exits setenv WFH_PIPELINE home bwagner WFU_Pipeline setenv WFU_PATH WFU_PIP E LINE WFU setenv WFU_SPM5 home bwagner spm5 setenv MATLABPATH WFU_PATH WFU_SPM5 The various elements that have been defined are DCMDICTPATH WFU_PIPELINE WFU_PATH WFU_SPMS5 MATLABPATH The location of the dictionary files needed by the DCMTK The location of the WFU_SPM5_PIPELINE The location of the WFU directory in the WFU SPM5 Pipeline The location of the SPM5 Additional paths that Matlab should load when it st
29. pported in newer Matlabs Running the included sample study First edit the WFU_PIPELINE ref_functions paradigm_lookup_table Replace the text home bwagner spm5_pipeline with the appropriate path to the pipeline Then see section 2 2 4 Autoprocessing DICOM images from the Command line DICOM images that have the paradigm number set 1 3 5 Considerations before compiling and using MoJoe MoJoe s intended use is on GE LX MRI scanners The MoJoe that is about to be built should run on the computer it has been compiled on However as scanners have very specific libraries and utilities available it may not run on the scanner If this occurs try to find make a computer with a similar configuration as the scanner Then follow these instructions again for making the DCMTK FLTK and MoJoe As a starting point please check the gcc version on the compiling computer and scanner by typing gcc version IMPORTANT NOTE Autoprocessing will stop after dicom conversion and 4D image creation if dicom field 0019 10e0 is not set to a valid reference function The method of setting this field varies by scanner and scanner usage policies If MoJoe is not to be installed please skip to section 1 3 11 Reference Functions 1 3 6 Compiling optional component FLTK required for MoJoe The MoJoe requires access to several libraries found in the DCMTK and the Fast Light Toolkit http www fltk org As the version of FLTK used w
30. r does not exist for the conversion a generic DICOM header structure is created and some user editable DICOM header fields are provided in the GUI to allow customization e g subject id study type 3 2 WFU Grid Distribution Tool In addition to the non interactive command line based pipeline we have also created a generic grid processing architecture GUI which allows automated distribution of MATLAB programs or scripts 21 WFU SPMS Pipeline v 1 0 maldjian wfubmce edu IWFU Grid Figure 3 WFU Grid Distribution Tool The user can choose the format of the input data list of filenames an image or loop the distribution partitioning scheme point slice or vector and the Matlab command to be distributed All processing information is stored in the Log Directory This is very useful for programs that need to run on many files or images for example preprocessing of MRI images for a VBM analysis on 30 subjects The only requirement of the MATLAB script to be distributed is that it be structured to take an index of values a binary image mask of voxels or list of filenames to operate on as input Our architecture takes advantage of the Sun Grid Engine array job task distribution feature The grid distribution tool is designed to take any appropriately written MATLAB function and distribute it on a computing cluster using the Sun Grid Engine array job feature Further information may be found in WFU_PIPELINE WF U WFU_grid
31. then a sample extract can be done The above screen should be available Simply click the start button to start processing 17 WFU SPM5 Pipeline v1 0 maldjian wfubmce edu 2 2 Autoprocessing 2 2 1 Autoprocessing from MoJoe Autoprocessing from MoJoe starts automatically from the completion of a Capture or Extract session Captured files p files are reconstructed starting by issuing a WFU_PIPELINE fmri autorecon_excite command on the ssh server Extracted files dicoms are processed by issuing a spm5_pipeline fmri autolocsort_excite_paradigm command on the ssh server Further details are found in the following sections 2 2 2 Autoprocessing P files from the Command line Autoprocessing of p files is done by the Matlab function wfu_recon m To simplify processing a ksh script can be run that will run this Matlab script and set applicable environmental variables WFU_PIPELINE bin wfu_RECON path pfile1 path pfile2 IMPORTANT NOTE WFU_PIPELINE WFU WF U_geToolbox recon wfu_recon m will need to be modified to suit p file reconstruction based on specific aims of the study As each type of reconstruction can vary widely this script is provided as a starting point for integrating your own p file reconstruction routines 2 2 3 Autoprocessing DICOM images from the Command line DICOM images that do not have the paradigm number set Processing DICOM images that do not have their paradigm number set DICOM field 0019 10e0 r
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