Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

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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mris_smooth
by Antao Du 27 Jul '05

27 Jul '05

Hi, When I run recon-all stage2, I got the following error message but I can't get the answer from the email list. Can anyone help me what is wrong? thanks, Antao ----- Starting Hemisphere rh -------- --------------------------------------------- Tessellate rh Wed Jul 27 10:23:11 PDT 2005 mri_tessellate /home/antao/freesurfer/subjects/AD1334/mri/filled 127 /home/antao/freesurfer/subjects/AD1334/surf/rh.orig /home/antao/freesurfer/subjects/AD1334/scripts warning: non-standard value for imnr1 (341, usually 256) in file /home/antao/freesurfer/subjects/AD1334/mri/filled/COR-.info warning: non-standard value for x (341, usually 256) in file /home/antao/freesurfer/subjects/AD1334/mri/filled/COR-.info warning: non-standard value for y (341, usually 256) in file /home/antao/freesurfer/subjects/AD1334/mri/filled/COR-.info slice 90: 99 vertices, 127 faces slice 100: 2834 vertices, 2979 faces slice 110: 8516 vertices, 8740 faces slice 120: 16580 vertices, 16896 faces slice 130: 26781 vertices, 27158 faces slice 140: 38001 vertices, 38396 faces slice 150: 49639 vertices, 50041 faces slice 160: 63118 vertices, 63551 faces slice 170: 74988 vertices, 75403 faces slice 180: 87067 vertices, 87498 faces slice 190: 98643 vertices, 99104 faces slice 200: 110528 vertices, 110958 faces slice 210: 120129 vertices, 120486 faces slice 220: 127451 vertices, 127723 faces slice 230: 133652 vertices, 133943 faces slice 240: 138604 vertices, 138817 faces slice 250: 139960 vertices, 140038 faces slice 260: 139960 vertices, 140038 faces slice 270: 139960 vertices, 140038 faces slice 280: 139960 vertices, 140038 faces slice 290: 139960 vertices, 140038 faces slice 300: 139960 vertices, 140038 faces slice 310: 139960 vertices, 140038 faces slice 320: 139960 vertices, 140038 faces slice 330: 139960 vertices, 140038 faces slice 340: 139960 vertices, 140038 faces using the conformed surface RAS to save vertex points... writing /home/antao/freesurfer/subjects/AD1334/surf/rh.orig --------------------------------------------- Smooth1 rh Wed Jul 27 10:23:30 PDT 2005 mris_smooth /home/antao/freesurfer/subjects/AD1334/surf/rh.orig /home/antao/freesurfer/subjects/AD1334/surf/rh.smoothwm /home/antao/freesurfer/subjects/AD1334/scripts Segmentation fault (core dumped) ERROR: mris_smooth exited with non-zero status ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on /dev/hda2 117037708 11360416 99732040 11% / ------------------------------------------ recon-all exited with errors at Wed Jul 27 10:23:31 PDT 2005

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Re: [Freesurfer] Freesurfer OS problems
by Hans Johnson 27 Jul '05

27 Jul '05

Bruce, Thanks for the reply. Yes we have a version of FreeSurfer running (Feb. 2004 + misc. patches that you provided through June 2004). The problem is that our working version FreeSurfer is only running on RedHat 9. We have one machine that we have not been allowed to upgrade because of this. We are trying to standardize on RH EL4 for all 60 of our computers, but freesurfer is the only application that we have not been able to install and work successfully. Additionally, we have purchased a few Macintosh computers that we are testing to see if they will work. A collaborative site (MIND at University of New Mexico) has a huge investment in Mac, and is very interested in using freesurfer on those machines. We are trying to make a common application platform between both our sites and across both Mac and RH EL4 platforms. Finally, we are hoping to do a lot of freesurfer investigations and integration with BRAINS this fall, and we would rather be near the bleeding edge than 2 years out of date during the finalization of a pipeline that will need to stay stable for the next few years. As always, your help is greatly appreciated. Thanks, Hans On 7/27/05 8:01 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Nick, > > could you help Hans get stuff installed? Hans: didn't you guys already > have a version running? > > thanks, > Bruce > > > On Wed, 27 Jul 2005, Hans Johnson wrote: > >> 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 >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >

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