Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30129 discussions

RE: [Freesurfer] mris_glm analysis
by Fornito, Alexander 04 Aug '05

04 Aug '05

Hi Nick, Sorry to keep bugging you about this, but I ran tyhe new script and got a slighlty different message (below). Any ideas? make_average_surface --subjects 1000186 1000187 1000188 --echo if ( 1 ) then set getting_subjects = 0 endif breaksw end while ( 1 != 0 ) set flag = --echo if ( ! 0 ) then shift endif switch ( --echo ) set echo = 1 if ( 0 ) then breaksw end while ( 0 != 0 ) goto parse_args_return goto check_params if ( ! 1 ) then if ( ! 1 ) then if ( ! -e /data/flanders/work/alex/freesurfer/subjects ) then if ( ! 1 ) then if ( ! -e /usr/local/freesurfer ) then goto check_params_return echo ==================== ==================== echo make_average_surface make_average_surface echo ==================== ==================== echo input subjects: 1000186 1000187 1000188 input subjects: 1000186 1000187 1000188 echo output subject: average output subject: average mkdir -p /data/flanders/work/alex/freesurfer/subjects/average /data/flanders/work/alex/freesurfer/subjects/average/surf /data/flanders/work/alex/freesurfer/subjects/average/mri /data/flanders/work/alex/freesurfer/subjects/average/mri/transforms /data/flanders/work/alex/freesurfer/subjects/average/mri/T1 /data/flanders/work/alex/freesurfer/subjects/average/mri/orig /data/flanders/work/alex/freesurfer/subjects/average/mri/label if ( -e /data/flanders/work/alex/freesurfer/subjects/average == 0 ) then mkdir -p /data/flanders/work/alex/freesurfer/subjects/average/surf endif set tmp_subjects = ( 1000186 1000187 1000188 ) cp /data/flanders/work/alex/freesurfer/subjects/1000186/mri/T1/COR-.info /data/flanders/work/alex/freesurfer/subjects/average/mri/T1 cp /data/flanders/work/alex/freesurfer/subjects/1000186/mri/orig/COR-.info /data/flanders/work/alex/freesurfer/subjects/average/mri/orig foreach hemi ( lh rh ) foreach c ( sulc curv ) echo mris_average_curvature... mris_average_curvature... mris_average_curvature sulc lh sphere.reg 1000186 1000187 1000188 ../average/surf/lh.avg_sulc processing subject 1000186... processing subject 1000187... processing subject 1000188... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory end echo mris_average_curvature... mris_average_curvature... mris_average_curvature sulc lh sphere.reg 1000186 1000187 1000188 ../average/surf/lh.avg_curv processing subject 1000186... processing subject 1000187... processing subject 1000188... MRISwriteCurvature: could not open ../average/surf/lh.avg_curv No such file or directory end foreach s ( orig white pial inflated ) echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface -i 7 -o orig lh orig_avg sphere.reg average 1000186 1000187 1000188 reading vertex positions from orig... processing subject 1000186... The following must be revisited********************************** Segmentation fault -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 7/27/2005 5:33 AM To: Goldman, Aaron (NIH/NIMH) Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] mris_glm analysis Aaron, Hi, can you tell me the version of make_average_surface you are running? Type: make_average_surface --version Just in case yours in out-of-date, I've attached the latest make_average_surface script, which should not have the SUBJECTS bug that you describe. The file is gzipped, so do the following: - copy the file to $FREESURFER_HOME/bin - change directory to $FREESURFER_HOME/bin - type: gunzip make_average_surface.gz Then you should be able rerun the make_average_surface utility. Nick On Tue, 2005-07-26 at 15:11 -0400, Goldman, Aaron (NIH/NIMH) wrote: > Hi, I’m trying to do a thickness analysis with mris_glm, and I had a > couple of questions: > > > > 1) I made an average surface using mris_make_average_surface, but I > won’t load it with tksurfer because it “could not find anatomical > header information.” Do you know how I can fix this? I also tried > “make_average_surface -subjects subject1… subject111,” but it said > SUBJECTS wasn’t defined, and wouldn’t run. > > > > 2) I’ve been able to successfully run a test mris_glm command using a > design file like: > > > > subject1 0 1 > > subject2 1 0 > > etc > > > > and the following commands: > > > > foreach h ( lh rh ) > > mris_glm --design $SUBJECTS_DIR/results/test_design.txt \ > > --surfmeas thickness \ > > --hemi $h \ > > --trgsubj Colin \ > > --nsmooth 300 \ > > --beta ${h}_test_beta bfloat \ > > --var ${h}_test_var bfloat > > mris_glm --design $SUBJECTS_DIR/results/test_design.txt \ > > --hemi $h \ > > --trgsubj Colin \ > > --beta_in ${h}_test_beta bfloat \ > > --var_in ${h}_test_var bfloat \ > > --gcv 1 -1 \ > > --sigt $SUBJECTS_DIR/Colin/surf/${h}_test_sigt > paint \ > > --t $SUBJECTS_DIR/$trgsubj/surf/${h}_test_t > paint > > end > > > > > > where a 1 in column 2 indicates one allele of the gene we’re studying, > whereas a 1 in column 3 indicates the other. However, I’d like to also > covary for age and gender, and I was wondering how I would need to > edit my design file and mris_glm commands to do that. > > > > Thanks, > > > > -Aaron- > > > > Aaron L. Goldman > > Post-Bacc IRTA > > Genes, Cognition and Psychosis Program, NIMH > > Building 10, Room 3C108 > > Phone: (301) 435-0944 > > Email: aarong(a)mail.nih.gov > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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command line problems with tkmedit/tksurfer
by David Soscia 02 Aug '05

02 Aug '05

Guys, I am having trouble getting volumes/surfaces to show when I use the command line to try to bring them up. Prior, I was just using the csurf interface to bring up all my volumes, but now that I've make my first final surface I'm trying to get the pial surface using the command line. I type in... tksurfer </up/to/the/directory/before/mri, surf, tmp, scripts, etc> lh pial (or others, they all dont work) and i get this error every time... tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory it does the same thing when i try to open something with tkmedit...any ideas on what the problem is? Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad(a)mail.amc.edu

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Scripts in TkSurfer
by Sarah Rugheimer 02 Aug '05

02 Aug '05

Hello, I have a question about creating scripts for TkSurfer. I really know next to nothing about scripts in general so these are rather basic questions. There seems to be a lot of scripting commands for TkMedit but not for TkSurfer. Is there a general list of the basic commands? The commands I need to know how to do are: Open a subject Load a surface (inflated and pial) Display the color bar in a for loop Overlay a .w file Redraw the image Save as a .rgb image end loop Is this all done in a csh script? And then how do I run the script? Thank you for any help. Sarah

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Overlay on cortical surface
by Arvind Gururajan 01 Aug '05

01 Aug '05

� Hello all, I was wondering if it possible to overlay functional data on to (pre-generated)cortical surface? Does freesurfer provide an option to functional/surface registration( I dont have any .cor data instead only .orig)? Could anyone please point out how this could be done? Thanks, Arvind Gururajan

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anatomical_stats
by Fornito, Alexander 30 Jul '05

30 Jul '05

Hi, Is there anyway to print the output of mri_anatomical_stats to a text file? Thanks, Alex

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problem with make_average_surfaces script
by Glenn Lawyer 29 Jul '05

29 Jul '05

Hi, When I run make_average_surface, the script fails on line 117. The line in the script is cp ${FREESURFER_HOME}/average/surf/${hemi}.sphere.reg . The error is "file not found" Should the line read cp ${FREESURFER_HOME}/subjects/average7/surf/${hemi}.sphere.reg . instead? It seems obvious to me, but thought it better to double-check I am using the 20040218 version of freesurfer, which has the following in the ${FREESURFER_HOME}/average directory: [shell] ls /usr/local/freesurfer/average/ lh.atlas2002_simple.gcs rh.atlas2002_simple.gcs rigidly_aligned_brain_template.tif lh.average.tif rh.average.tif talairach_mixed.gca lh_trans_toSulc.gcs rh_trans_toSulc.gcs tissue_parms.txt Thanks, +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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difficultly generating talairach.m3z
by Elizabeth Fenstermacher 29 Jul '05

29 Jul '05

Hello All, One of our collaborators is trying to generate the talairach.m3z and is running into great difficulties doing so. It seems like the only necessary input is the talairach.xfm, but even after running stage2 independently a second time it did not generate? Has anyone every encountered this difficulty? They are trying to actually generate it by today in order to get some eTIV volumes for a paper that is being submitted, so please let me know soon! Thanks Eliz

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can't seem to source dev env
by Tamara Knutsen 29 Jul '05

29 Jul '05

/usr/local/freesurfer/nmr-dev-env: No such file or directory. is anyone else getting this error this morning? i already rebooted my computer...not sure what else it could be. thanks, tamara

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recon-all error
by Colleen Kristen Tuffy 28 Jul '05

28 Jul '05

Hi FreeSurfer Gurus, I recently moved from using a linux-based FreeSurfer to one of the newer Darwin distributions. I've been following the tutorial at http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsTutorial/morphAndReco…, but my cortical reconstruction was failing on -autorecon2 with the following error: --------------------------------------------- Intensity Normalization2 Thu Jul 14 23:51:48 PDT 2005 /Volumes/Storage/data/freesurfer/subjects/clda/mri mri_normalize -mask brain nu.mgz T1.mgz reading from nu.mgz... corRead(): can't open file /Volumes/Storage/data/freesurfer/subjects/clda/mri/brain/COR-.info mri_normalize: could not open mask volume brain. using MR volume brain to mask input volume... ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Thu Jul 14 23:51:54 PDT 2005 ============================================= So I installed a newer recon-all from Doug's outgoing ftp directory (timestamp 7/26/05) that Russ Poldrack recommended. This one crashed (seg fault) after initial inflation, during topology correction, I think. I have attached a copy of the most recent log file. I am running panther on a G5 with two 2.5 GHz CPUs and 4 GB of memory. Please let me know what other information you might need. Thanks for any advice, Colleen Tuffy Human Neuroimaging Lab University of Oregon

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tkregister2 help
by Tracy Wang 28 Jul '05

28 Jul '05

Hi all, I'm trying to run tkregister2 and I have the following questions: 1. It seems to look for a talairach directory in the main subject directory. Does this mean I have to make/modify this directory each time i want the tkregister2 to manually correct the talairach transform? 2. when tkregister tries to initialize, it tries to read the talairach.xfm file, but it's not finding the talairach.xform. What does this mean? Here is the error output: tkregister2 --mgz --s 000112_vc1552_test --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.35 2005/07/12 19:50:28 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 0.874 -0.173 -0.004 -3.334; 0.188 0.957 -0.284 -10.880; 0.046 0.217 0.760 31.928; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/Users/Shared/freesurfer/subjects/00112_vc1552_test/mri/transforms/ talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /Users/Shared/freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /Users/Shared/freesurfer/subjects/talairach/mri/orig as 0 Thanks for any assistance! Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

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