Freesurfer

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GLM analysis question
by Avram Holmes 13 Dec '06

13 Dec '06

FSFast support folks, I am looking for some support running an analysis in FSFast. As far as we can tell we have successfully run every step in a random effects analysis but we are having trouble viewing/interpreting the results. I was hoping that I would be able to post my processing stream and see if anyone would give us feedback on what we have or havent done correctly (see below). My understanding is that after I run mkanalysis-sess.new, selxavg-sess, mkcontrast-sess, stxgrinder-sess, and isxavg-re-sess, I have fit a model to the data and I am testing the fit of the model across our contrasts. However, Im not seeing the expected effects and I am wondering if I am missing a step or if my stream is not optimized. I have spent a considerable amount of time searching the wiki page and I havent been able to track down a detailed description of how to conduct and interpret a complete GLM analysis in FSFast so I am a little unsure if I have everything correct. Any help would be greatly appreciated, Avram #! /bin/csh -f Step1 set mypath = . set sub = $1 mc-sess -fstem f -fmcstem fmc -s ${sub} -d ${mypath} stc-sess -i fmc -o fmcstc -so siemens -s ${sub} -d ${mypath} spatialsmooth-sess -i fmcstc -o fmcstcsm5 -fwhm 5 -d ${mypath} -s ${sub} mkbrainmask-sess -s ${sub} -d ${mypath} Step2 set analysis = 'moneygamma_test' set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07 FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15 FPPREW16 FPPREW17 FPPREW18' mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5 -paradigm moneygame.par -designtype event-related -timewindow 30 -funcstem fmcstcsm5 -nconditions 5 -polyfit 1 -mcextreg -taumax 20 -mask brain foreach s ($subj) selxavg-sess -s ${s} -d . -analysis ${analysis} end mkcontrast-sess -analysis ${analysis} -contrast omnibus -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 -nosumconds mkcontrast-sess -analysis ${analysis} -contrast pun_v_noinc -a 1 -c 2 mkcontrast-sess -analysis ${analysis} -contrast rew_v_noinc -a 3 -c 2 mkcontrast-sess -analysis ${analysis} -contrast pun_v_rew -a 1 -c 3 mkcontrast-sess -analysis ${analysis} -contrast rew_v_pun -a 3 -c 1 foreach s ($subj) autoreg-sess -d . -s ${s} -fsd bold end Step3 set mypath = . set analysis = 'moneygamma_test' set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07 FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15 FPPREW16 FPPREW17 FPPREW18' foreach s ($subj) stxgrinder-sess -contrast omnibus -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast pun_v_noinc -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast rew_v_noinc -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast pun_v_rew -analysis ${analysis} -s ${s} -d ${mypath} stxgrinder-sess -contrast rew_v_pun -analysis ${analysis} -s ${s} -d ${mypath} end Step4 set analysis = 'moneygamma_test' set subj = 'FPPREW01 FPPREW02 FPPREW03 FPPREW04 FPPREW05 FPPREW06 FPPREW07 FPPREW08 FPPREW09 FPPREW10 FPPREW11 FPPREW12 FPPREW13 FPPREW14 FPPREW15 FPPREW16 FPPREW17 FPPREW18' set glist = 'GROUPLIST' set group = 'Controls' set contrasts = 'omnibus pun_v_noinc rew_v_noinc pun_v_rew rew_v_pun' foreach s ($subj) foreach anal ($analysis) func2tal-sess -res 4 -analysis ${anal} -d . -s ${s} foreach hemi (lh rh) func2sph-sess -analysis ${anal} -hemi ${hemi} -projfrac .3 -d . -s ${s} sphsmooth-sess -smoothsteps 10 -analysis ${anal} -insphdir sph -outsphdir sphsm10 -hemi ${hemi} -d . -s ${s} end end end foreach c ($contrasts) isxavg-re-sess -analysis ${analysis} -group ${group} -space tal -d . -sf ${glist} -contrast ${c} foreach hemi (lh rh) isxavg-re-sess -analysis ${analysis} -group ${group} -space sph -hemi ${hemi} -d . -sf ${glist} -contrast ${c} end end ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [Freesurfer] A Possible Bug in Making Labels in Tksurfer
by Reza Rajimehr 13 Dec '06

13 Dec '06

Hi Kevin, on machine monkeylove source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects cd /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/Human_Eccen/Katie/MYSTUDY surf-sess -sf sf.txt -df df.txt -analysis Analysis_Human_Eccen -contrast 123456 -map sig -hemi rh I changed the min threshold to 4 (linear) in the Tksurfer window (view - config overlay ...). Reza > Thanks for this report. Can you point me at the data you were using, > whether you were using the std or dev environment, and what command > you used to start tksurfer? > > On Tue, Dec 12, 2006 at 11:28:45PM -0500, Reza Rajimehr wrote: >> Hi (Doug, Kevin, ...), >> >> I am experiencing a problem with making labels in Tksurfer (for doing a >> subsequent ROI analysis). I did something as follows: >> >> 1) I loaded a functional activity map by surf-sess (human cortex). >> >> 2) Then, I loaded the full flattened cortical surface. >> >> 3) After right-clicking in the Tksurfer window, I clicked >> (left-clicking) >> on the center of 4 spatially distinct activity patches (i.e. 4 yellow >> spots of activity, which had no overlap with each other and no overlap >> with other yellow or blue patches). So 4 vertices were selected (as I >> saw >> in the command-line window). >> >> 4) Then, I openned the "Custom Fill" dialog box, and selected the >> following options: >> >> Fill Conditions: Up to and including paths, Up to functional values >> below >> threshold >> >> Fill From: All marked vertices >> >> Action: Create a new label >> >> After clicking the "Fill" button (in the "Custom Fill" dialog box) and >> then clicking the "Mark Label" button (in the Tksurfer window), the 4 >> patches were appropriately selected as white labels. In the command-line >> window: >> >> % surfer: filling (ctrl-c to cancel).. done, 123 vertices filled >> surfer: filling (ctrl-c to cancel)... done, 542 vertices filled >> surfer: filling (ctrl-c to cancel). done, 105 vertices filled >> surfer: filling (ctrl-c to cancel)..... done, 954 vertices filled >> >> 5) I saved the selected label. In the command-line window: >> >> writing 2913 labeled vertices to >> /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects/katie/label/DFPRHKAS.label. >> >> >> The problem is that the number of saved vertices is much more than the >> sum >> of vertices in the 4 patches (2913 vs. 123+542+105+954). I do not have >> this problem when I click on just 2 patches (rather than 4), and the >> number of saved vertices is the sum of vertices in the 2 patches. I also >> had this problem before, and I am worried that some additional vertices >> (voxels) are saved out of my control, which might affect the ROI >> analysis. >> >> Thanks for any help, >> >> Best, >> Reza >> >> ******************************** >> Reza Rajimehr, MD >> >> NMR Athinoula A. Martinos Center >> Department of Radiology >> Massachusetts General Hospital (MGH) >> Building 149, 13th St. >> Charlestown, MA 02129 >> >> Email: reza(a)nmr.mgh.harvard.edu >> ******************************** >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Kevin Teich ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

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A Possible Bug in Making Labels in Tksurfer
by Reza Rajimehr 12 Dec '06

12 Dec '06

Hi (Doug, Kevin, ...), I am experiencing a problem with making labels in Tksurfer (for doing a subsequent ROI analysis). I did something as follows: 1) I loaded a functional activity map by surf-sess (human cortex). 2) Then, I loaded the full flattened cortical surface. 3) After right-clicking in the Tksurfer window, I clicked (left-clicking) on the center of 4 spatially distinct activity patches (i.e. 4 yellow spots of activity, which had no overlap with each other and no overlap with other yellow or blue patches). So 4 vertices were selected (as I saw in the command-line window). 4) Then, I openned the "Custom Fill" dialog box, and selected the following options: Fill Conditions: Up to and including paths, Up to functional values below threshold Fill From: All marked vertices Action: Create a new label After clicking the "Fill" button (in the "Custom Fill" dialog box) and then clicking the "Mark Label" button (in the Tksurfer window), the 4 patches were appropriately selected as white labels. In the command-line window: % surfer: filling (ctrl-c to cancel).. done, 123 vertices filled surfer: filling (ctrl-c to cancel)... done, 542 vertices filled surfer: filling (ctrl-c to cancel). done, 105 vertices filled surfer: filling (ctrl-c to cancel)..... done, 954 vertices filled 5) I saved the selected label. In the command-line window: writing 2913 labeled vertices to /space/ship/4/users/Retinotopy_Project/Human_Retinotopy/subjects/katie/label/DFPRHKAS.label. The problem is that the number of saved vertices is much more than the sum of vertices in the 4 patches (2913 vs. 123+542+105+954). I do not have this problem when I click on just 2 patches (rather than 4), and the number of saved vertices is the sum of vertices in the 2 patches. I also had this problem before, and I am worried that some additional vertices (voxels) are saved out of my control, which might affect the ROI analysis. Thanks for any help, Best, Reza ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

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mri_surf2surf
by Lars M. Rimol 12 Dec '06

12 Dec '06

Hi, I want to resample a number of subjets' (e.g.) thickness files to ico (atlas space). It seems that mir_surf2surf has been changed, can I still use a list of subject names to specify the subjects with the flag --f? Also, what is source and what is target? I assume source is the file that is mapped onto the target, so that the output file will contain the data from the source file in the coordinate system of the target file? I used this command line to resample subject 20543 to ico: mri_surf2surf --hemi lh --srcsubject subj20543 --srcsurfval thickness --src_type curv --trgsubject ico --trgicoorder 7 --trgsurfval TEST.mgh If I want to do this with a list of subjects, is there any way to specify such a list on the command line? Is --src_type curv correct? Is this flag valid for both thickness files, sulc files, any type of .mgh files (if I e.g. calculate some ratio based on a set of surface files and store the result as an .mgh)? Can I use make_average_subject and use -trgsubject <average_subject> instead of -trgsubject ico Would that make any difference? Thank you! Lars -- yours, LMR

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surface coil intensity normalisation and 3.0.4
by Sebastian Moeller 12 Dec '06

12 Dec '06

Hi Doug, hi list, recently you implemented a version of mri_nu_correct.mni for me that allows for better settings for surface coil recordings. I dragged your change from 3.0.3 into 3.0.4 and just now realised, that it did not do anything ;), as the recon-all script in 3.0.4 does not process xopts for mri_nu_correct.mni. I guess in 3.0.3 I used the hacked version of nu_correct to hide the fact that recon-all dropped the xopts on the floor, oh my. Anyway recon-all of 3.0.4 only requires the following two edits: line 520 insert: set xopts = `fsr-getxopts mri_nu_correct.mni $XOptsFile`; and then replace the original line 521, now line 522 with the following: --o nu.mgz --n $NuIterations $xopts) (basically this adds "$xopts to the creation of cmd"). then it works like it expected. Thanks for all the tools & the support Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Run Freesurfer on a supercomputer
by Juergen Haenggi 12 Dec '06

12 Dec '06

Dear Freesurfer user because Freesurfer is so processor and memory intensive, we intented to run Freesurfer parallely on a supercomputer (called Matterhorn Cluster http://www.id.unizh.ch/dl/wissrechnen/HPC-Supercomputing-Main.html) Does Freesurfer is able to run on such a machine without modifying it? What are potential problems that could occur? Thanks in advance Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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problem after moving data
by Nicolas Cherbuin 12 Dec '06

12 Dec '06

Dear Freesurfers, I processed a large number of scans with autorecon-all on a linux cluster. I then moved the data to a usb drive for further analysis. I had no problem viewing the analysed scans with tkmedit although it seemed to search for talairach.xfm on the old path before trying in the current directory. However, tksurfer does not work and gives the error "Couldn't create output file .xdebug_tksurfersurfer". How do I fix this problem? I have tried to copy one subject to the local hard drive and view it from there but it did not help. Thanks for your help Regards Nic

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version 3.0.2
by Chacko Cherian 10 Dec '06

10 Dec '06

Hello all, I'd like to know whether the good_output and bert, analysis were done on version 3.0.2? If so could anyone please pass me a link to that version? Thanks Chacko. ____________________________________________________________________________________ Have a burning question? Go to www.Answers.yahoo.com and get answers from real people who know.

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how to extract a piece of cortical surface...
by Shahabuddin Ansari 09 Dec '06

09 Dec '06

Hello, I am working on nonlinear registration of cortical surface and subcortical volumes. I am able to extract individual subcortical objects from the freesurfer segmentation for registration, but don't know how to extract a patch from cortical surface. Could somebody guide me please? Thanks Shahab --------------------------------- Access over 1 million songs - Yahoo! Music Unlimited.

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talairach log file
by Paul Greenberg 08 Dec '06

08 Dec '06

Hi all, In each subject's /mri/transforms/talairach.log file, there are 6 instances of output for the "Final objective function value", which one reflects the quality of the final output? The last one? Thanks, Paul Greenberg

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