are you sure the label file is really a label file? Does the same thing happen if you specify -l labelfile on the command line?
On 04/18/2016 05:08 PM, DeCross, Stephanie N. wrote: > I can open the nii.gz output of the first step (vol2vol) just fine. But the > .label output of the second step (cor2label) won't open in tksurfer or > freeview. When I try to open it in freeview from the command line (freeview > -l <nameoflabel.label>) I get: > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC > ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to > find memory corruption errors > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run > [0]PETSC ERROR: to get more information on the crash. > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 > CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Unknown Name on a linux-gnu named > anderson.nmr.mgh.harvard.edu by sdecross Mon Apr 18 17:03:37 2016 > [0]PETSC ERROR: Libraries linked from > /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc > --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 > --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown > file > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > > When I try to open the .label file in tksurfer by putting in the command line > "tksurfer fsaverage lh inflated" and then opening the label menu, the > tksurfer command line reads this before it automatically closes: > > subject is fsaverage > hemi is lh > surface is inflated > surfer: current subjects dir: > /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53 > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: > /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/ROIs/AllROIs/temp/VoltoSurf > checking for nofix files in 'inflated' > Reading image info > (/autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage) > Reading > /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage/mri/orig.mgz > surfer: Reading header info from > /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage/mri/orig.mgz > surfer: vertices=163842, faces=327680 > surfer: single buffered window > surfer: tkoInitWindow(fsaverage) > surfer: using interface /usr/local/freesurfer/stable5_3_0/tktools/tksurfer.tcl > Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl > Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl > Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl > Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > % ******************** 0 nonzero vertices found ******************** > label stat field identically zero - setting to 1 > 12304 unassigned vertices in label - building spatial LUT... > assigning vertex numbers to label... > MatrixMultiply: m2 is null! > > > Thanks, > Stephanie > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, April 13, 2016 5:10 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert > MNI152 ROI to FreeSurfer label > > what is your tksurfer command line? Can you send all the terminal output > from tksurfer? Does it work in freeview? > > On 04/13/2016 11:20 AM, DeCross, Stephanie N. wrote: >> Hi, >> >> I’m trying to take an ROI in MNI152 volume space and make it into a >> cortical surface label, for visualization purposes. >> >> With my input being the lh thresholded, binarized MNI152 nii.gz label >> (when I visualize it, it looks as it should in fslview), I ran: >> >> mri_vol2vol -- mov <labelinput.nii.gz> -- targ >> $SUBJECTS_DIR/fsaverage/mri/orig.mgz -- o <outputname.nii.gz> -- >> regheader -- talres 2 -- interp nearest >> * >> * >> mri_cor2label -- c <outputname.nii.gz from above> -- id 1 -- l >> ./<newoutputname.label> >> * >> * >> My commands above seem to have run fine, but when I open the lh in >> tksurfer and try to load the new lh label file, the dialogue runs for >> a little but then errors out: >> >> 12304 unassigned vertices in label - building spatial LUT… >> assigning vertex numbers to label... >> MatrixMultiply: m2 is null! >> >> And then tksurfer closes. I’m not sure what’s going wrong - does >> anyone have any pointers or troubleshooting methods I can try? >> >> Thanks, >> Stephanie >> >> *Stephanie N. DeCross* >> Clinical Research Coordinator >> Psychiatric Neuroimaging Research Program >> Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> 149 13th Street, Rm 2620A >> Charlestown, MA 02129 >> Phone: (617) 724-3283 >> Fax: (617) 726-4078 >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
