Freesurfer July 2005

freesurfer@nmr.mgh.harvard.edu

39 participants
68 discussions

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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RE: [Freesurfer] mris_glm analysis
by Fornito, Alexander 27 Jul '05

27 Jul '05

Hi Nick, I tried running the script you attached to this thread, and the error was similar, albeit slightly different (see below). Any ideas? Thanks, Alex make_average_surface --subjects 1000186 1000187 1000188 --out test_avg --echo 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: test_avg output subject: test_avg mkdir -p /data/flanders/work/alex/freesurfer/subjects/test_avg /data/flanders/work/alex/freesurfer/subjects/test_avg/surf /data/flanders/work/alex/freesurfer/subjects/test_avg/mri /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/transforms /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/T1 /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/orig /data/flanders/work/alex/freesurfer/subjects/test_avg/mri/label if ( -e /data/flanders/work/alex/freesurfer/subjects/test_avg == 0 ) then mkdir -p /data/flanders/work/alex/freesurfer/subjects/test_avg/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/test_avg/mri/T1 cp /data/flanders/work/alex/freesurfer/subjects/1000186/mri/orig/COR-.info /data/flanders/work/alex/freesurfer/subjects/test_avg/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 ../test_avg/surf/lh.avg_sulc processing subject 1000186... processing subject 1000187... processing subject 1000188... MRISwriteCurvature: could not open ../test_avg/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 ../test_avg/surf/lh.avg_curv processing subject 1000186... processing subject 1000187... processing subject 1000188... MRISwriteCurvature: could not open ../test_avg/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 test_avg 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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mris_glm analysis
by Goldman, Aaron (NIH/NIMH) 26 Jul '05

26 Jul '05

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 <mailto:aarong@mail.nih.gov>

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tkregister problem
by Tamara Knutsen 26 Jul '05

26 Jul '05

for data acquired using the multiecho sequence and undistorting it using anders' program, i get oversaturated images in the tkregister program, making it impossible to register to the anatomical. however i took other in-session functionals that i can use to register successfully. but if i copy these register.dat files into the bold directory and try to use them to paint the activation maps onto the anatomical surfaces, and then try to view the surfaces, i get a segmentation fault. for instance, in /space/annecy/19/users/knutsen/050126Edgar i created the register.dat using the MErecon/005 and copied this into the bold directory. then ran the paint.csh and surf-lh.csh scripts in the scripts directory and got this segmentation fault: [whatever:scripts] (nmr-dev-env) csh -f paint.csh cat: /usr/local/freesurfer/dev/fsfast/docs/version: No such file or directory ----------------------------------------------------------------- paint-sess logfile is /autofs/space/annecy_019/users/knutsen/050126Edgar/mystudy/log/paint-sess.log ----------------------------------------------------------------- INFO: painting onto white grep: /autofs/space/annecy_019/users/knutsen/050126Edgar/session.info: No such file or directory SpaceDir is SpaceSubDir is INFO: setting srcsubject to Fri Jul 22 11:04:56 EDT 2005 SpaceDir is INFO: Painting onto edgar2 Using Float2Int = round ---------------------------------------- /autofs/space/annecy_019/users/knutsen/050126Edgar/mystudy mri_vol2surf --srcvol /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig --src_type bfloat --srcreg /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/register.dat --surf white --hemi lh --projfrac 0 --frame 0 --out_type paint --float2int round --mapmethod nnf --o /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-lh.w --nvox /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/white-lh.nvox ---------------------------------------- INFO: output format is paint srcvol = /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig srctype = bfloat srcreg = /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh interp = nearest float2int = round INFO: float2int code = 0 INFO: bvolumeRead: min = -8.91759, max = 14.6838 Done loading volume Reading surface /space/orsay/2/knutsen//edgar2/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 76996/150625 Done mapping volume to surface Number of source voxels hit = 4931 avg = 0.410, stdev = 1.414, min = -6.978, max = 10.800 Fri Jul 22 11:05:00 EDT 2005 SpaceDir is INFO: Painting onto edgar2 Using Float2Int = round ---------------------------------------- /autofs/space/annecy_019/users/knutsen/050126Edgar/mystudy mri_vol2surf --srcvol /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig --src_type bfloat --srcreg /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/register.dat --surf white --hemi rh --projfrac 0 --frame 0 --out_type paint --float2int round --mapmethod nnf --o /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-rh.w --nvox /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/white-rh.nvox ---------------------------------------- INFO: output format is paint srcvol = /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig srctype = bfloat srcreg = /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh interp = nearest float2int = round INFO: float2int code = 0 INFO: bvolumeRead: min = -8.91759, max = 14.6838 Done loading volume Reading surface /space/orsay/2/knutsen//edgar2/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface vol2surf_linear: nhits = 72327/148729 Done mapping volume to surface Number of source voxels hit = 4443 avg = 0.391, stdev = 1.336, min = -6.783, max = 9.580 ---------------------------------------------------------- Fri Jul 22 11:05:03 EDT 2005 paint-sess completed SUCCESSFULLY [whatever:scripts] (nmr-dev-env) csh -f surf-lh.csh cat: /usr/local/freesurfer/dev/fsfast/docs/version: No such file or directory grep: /autofs/space/annecy_019/users/knutsen/050126Edgar/session.info: No such file or directory ----------------------------------------------------------------- surf-sess logfile is /autofs/space/annecy_019/users/knutsen/050126Edgar/mystudy/log/surf-sess.PPA.pl_fa.log ----------------------------------------------------------------- ------------------------------------------------------ ------------------------------------------------------ Session: 050126Edgar ---- ------ lh hemisphere ------ grep: /autofs/space/annecy_019/users/knutsen/050126Edgar/session.info: No such file or directory wfile is /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-lh.w ------------ tcl file ----------- set val /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-lh.w sclv_read_binary_values 0 set curv lh.curv read_binary_curv; set curvflag 1; source /usr/local/freesurfer/dev/lib/tcl/readenv.tcl open_window rotate_brain_y 90 sclv_set_current_field 0 redraw --------------------------------- ---------------------------------------------------------- /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA/pl_fa tksurfer -edgar2 lh inflated -tcl /tmp/surf-sess-18404.tcl ---------------------------------------------------------- Segmentation fault Fri Jul 22 11:05:10 EDT 2005 -- Tamara Knutsen http://www.nmr.mgh.harvard.edu/~knutsen

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new FreeSurfer release running on FC1?
by Renat Yakupov 26 Jul '05

26 Jul '05

Hello. I noticed that there are two Linux distribution of new FreeSurfer version, one for FC2 and one for RH9. Has anybody been able to run it on Fedora Core 1? When I try to run it, it says it needs tixwish, but tixwish needs tcl-8.4 which in turn needs glibc-2.3.4, and looks like there is no glibc-2.3.4 for Fedora Core 1. Any ideas will be appreciated. Thank you! Regards, Renat.

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New FreeSurfer Version
by David Soscia 26 Jul '05

26 Jul '05

Hey Guys, Has the new version of FreeSurfer been released yet? I spoke with Dr. Killiany at BU two Fridays ago and he told me it was going to be released very soon. If so, where can I get it because I don't see it anywhere on the FreeSurfer dowload page. Thanks, 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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Convexity value
by XJ Kang 25 Jul '05

25 Jul '05

Hi, What are the units of "convexity" values (the last column) in ?h.sulc.asc? Probably in mm? The values are <+- 1. It seems the values are two small for "the signed distance" that a vertex moves during the inflation process. Thanks. XJ

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Freesurfer July 2005