Freesurfer

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30063 discussions

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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MNI
by Timothy O'Keefe 25 Jul '05

25 Jul '05

After generating a cortical surface rendering, I would like to overlay my EPI activation maps. I considered rendering a cortical surface for all my participants but, they are all normalized to MNI space. Despite the structural variabilities which remain even after normalization, is it still common for people to use a single FreeSurfer rendering for visualization (given all your EPI data are also normalized to MNI)? -T

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Re: [Freesurfer] Tksurfer: Unable to view .orig file
by Arvind Gururajan 24 Jul '05

24 Jul '05

Hi Bruce, I found out what was wrong. If any of you had the same problem, it could be due to this. Vertices for freesurfer are in millimeters, and I had them in meters. Thanks for your help and good luck with the course. Arvind On 22 Jul 2005, Bruce Fischl wrote: > Hi Arvind, > > it's the middle of the FSL/FreeSurfer course, so we're all really busy. > Hopefully we'll get to it next week. > > Bruce > On Thu, 21 Jul 2005, Arvind Gururajan > wrote: > > > Hi, > > > > Could anyone please tell me what could be wrong? What more information do I > > need to provide? Your help will be really appreciated. > > > > Arvind Gururajan > > > > On 20 Jul 2005, Arvind Gururajan wrote: > >> Hi Bruce, > >> > >> I had a single file with both hemisphere data points. Was able to make a > >> crude separation into two hemisphere. Probably couldn't have messed up > >> here, I used a different software to visualize them, and it was fairly > >> clean separation. > >> > >> I used the following command to convert from .asc to .orig. > >> > >> mris_convert > >> /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.curv.asc > >> /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.orig > >> > >> .xdebug_tksurfer for the subject is empty, here it is anyways. > >> > >> Thanks for your help. > >> > >> Arvind > >> > >> > >> On 14 Jul 2005, Bruce Fischl wrote: > >>> Hi Arvind, > >>> > >>> you need to give us more info, and the .xdebug_tksurfer files. > >>> > >>> Bruce > >>> On Thu, 14 > >>> Jul 2005, Arvind Gururajan wrote: > >>> > >>>> Hi, > >>>> > >>>> I have trouble viewing .orig files in Tksurfer. I used mris_convert > > to > >>>> generate .orig files from .ascii( with number of vertices and > > triangles > >> for > >>>> each hemisphere). Any quick thoughts on what could be wrong ? No > > error > >>>> messages. > >>>> > >>>> Help would be appreciated. > >>>> > >>>> Arvind Gururajan > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >> > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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problem with recon-all
by Russ Poldrack 24 Jul '05

24 Jul '05

hi folks - I'm trying to get freesurfer (the latest Tiger snapshot) working on my mac but I'm having a problem with recon-all. If I try to apply it to the bert data included in the distribution, it seems to set up ok but then it doesn't actually do anything. here is the output from "recon-all-nmr -all -subjid bert" (same thing happens if I just use recon-all): Fri Jul 22 13:33:27 PDT 2005 /Users/Shared/freesurfer/bin//recon-all-nmr -all -subjid bert /Users/Shared/freesurfer/subjects/bert subjid bert SUBJECTS_DIR /Users/Shared/freesurfer/subjects FREESURFER_HOME /Users/Shared/freesurfer AutoSeg Enable = 1 Darwin ######################################## program versions used $Id: recon-all-nmr,v 1.71 2005/07/11 22:46:53 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 b ert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/ minctracc.c,v 96.11 2004/ 02/12 05:54:22 rotor Exp $ !p$Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19 :02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:4 9 bert Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using COR format here it just stops, which is presumably not the expected behavior with the -all flag. I also tried with a new dataset converted to mgz format and with the -autorecon1 option and the same thing happens. Any ideas what might be going on here? 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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mgz file format?
by Renat Yakupov 22 Jul '05

22 Jul '05

Hi everybody, I noticed the new FreeSurfer tutorial on the website and all 3D volumes are specified as *.mgz files there. What happened to old COR format? Is mgz the format of the new FreeSurfer distribution that is supposed to come out soon? Best, Renat.

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