Freesurfer

freesurfer@nmr.mgh.harvard.edu

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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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more on make_average_surface
by Glenn Lawyer 28 Jul '05

28 Jul '05

Hi, Sorry, another question on make_average_surface. after averaging the curvatures and the surfaces, the script moves to the surf directory: cd ${SUBJECTS_DIR}/${average_subject}/surf However, it does not return to the top directory before the second iteration of the foreach hemi (lh rh) loop. This gives me the following output when processing the rh: MRISwriteCurvature: could not open ../average/surf/rh.avg_sulc This suggests that MRISwriteCurvature expects to be one directory below the subjects directory. Finally, my question: Would it be better to modifiy the script so that the first command in the foreach hemi (lh rh) loop is cd ${SUBJECTS_DIR}/${average_subject} ? +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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Average Brain atlas
by Tracy Wang 27 Jul '05

27 Jul '05

Hi all, I was just wondering what the difference is between the talairach_mixed.gca, talairach_mixed_a1_new_b.gca and talairach_mixed_new_b.gca Thanks! Tracy Wang 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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Freesurfer OS problems
by Hans Johnson 27 Jul '05

27 Jul '05

Hello Freesurfer Developers, We are attempting to install freesurfer as one of our standard image processing packages at the Mental Health Clinical Research Center Image Processing Lab at The University of Iowa. Our environment consists of Redhat EL3WS, Redhat EL4WS, and MacOSX 10.4 operating systems. I could only find a matching MacOSX version of the software. Will the Redhat series of OS be supported? Additionally, I am attempting to install freesurfer on Mac OS X 10.4, but after the installer spends several minutes installing, it reports "There were errors installing the software" "Please try installing again". Your help and advise is greatly appreciated. Thanks, Hans J. Johnson, PhD Director of Image Processing The Department of Psychiatry, The University of Iowa

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Perl problems with mac install
by Russ Poldrack 27 Jul '05

27 Jul '05

hi folks - I wanted to let you know that the tiger snapshot installer for mac doesn't properly install the perl libraries needed for some of the MNI tools. I was able to get things to work by copying the relevant files into /System/Library/Perl/5.8.6, but I assume that you want the installer to do this automagically. cheers russ --- Russell A. Poldrack, Ph.d. Assistant Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563 phone: 310-794-1224 fax: 310-206-5895 email: poldrack(a)ucla.edu web: www.poldracklab.org

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