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
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
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#Sig... 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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 greve@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
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#Sig... 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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@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 greve@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
I think it’s really a label file? I took my binarized nii.gz and ran
mri_cor2label -- c NAME.nii.gz -- id 1 -- l ./newname.label
and I was under the impression that this turned it into a label file.
Yes, I get exactly the same errors when I try to open the label in both programs from the command line.
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
On Apr 19, 2016, at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
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#Sig... 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, April 13, 2016 5:10 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@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 greve@nmr.mgh.harvard.edumailto:greve@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
can you send me the label file?
On 04/20/2016 10:49 AM, DeCross, Stephanie N. wrote:
I /think/ it’s really a label file? I took my binarized nii.gz and ran
mri_cor2label -- c NAME.nii.gz -- id 1 -- l ./newname.label
and I was under the impression that this turned it into a label file.
Yes, I get exactly the same errors when I try to open the label in both programs from the command line.
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
On Apr 19, 2016, at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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#Sig... 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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, April 13, 2016 5:10 PM To: freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu mailto:greve@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
Sure! In case it's helpful, here are the 3 files for the steps of what I ran.
(1) lh_V1_Juelich_thr50_binarized.nii.gz is my original nii.gz file from the Juelich atlas, thresholded at 50 and binarized
(2) Then I ran the below mri_vol2vol command with that nii.gz, which gave me the output lh_V1_Juelich_thr50_binarized_voltosurf.nii.gz
(3) Then with that binarized_voltosurf.nii.gz file as the input, I ran the below mri_cor2label command, which gave me the output lh_V1_Juelich_thr50_binarized_voltosurf.label (the label file that won't open)
Thanks!! Steph
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, April 20, 2016 11:13 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label
can you send me the label file?
On 04/20/2016 10:49 AM, DeCross, Stephanie N. wrote:
I /think/ it’s really a label file? I took my binarized nii.gz and ran
mri_cor2label -- c NAME.nii.gz -- id 1 -- l ./newname.label
and I was under the impression that this turned it into a label file.
Yes, I get exactly the same errors when I try to open the label in both programs from the command line.
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
On Apr 19, 2016, at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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#Sig... 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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, April 13, 2016 5:10 PM To: freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu mailto:greve@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 greve@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
Play around more with my .label file, I realized that while it wouldn’t open in tksurfer or freeview, it DID open in tkmedit. So, I ran
mri_label2label -- srclabel <LabelThatOpenedInTkmedit.label> -- s fsaverage -- trglabel ./<LabelOnPial.label> -- hemi lh -- paint 30 pial -- trgsurf pial
and now it opens on tksurfer!
Best, 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
On Apr 21, 2016, at 11:29 AM, DeCross, Stephanie N. <sdecross@mgh.harvard.edumailto:sdecross@mgh.harvard.edu> wrote:
Sure! In case it's helpful, here are the 3 files for the steps of what I ran.
(1) lh_V1_Juelich_thr50_binarized.nii.gz is my original nii.gz file from the Juelich atlas, thresholded at 50 and binarized
(2) Then I ran the below mri_vol2vol command with that nii.gz, which gave me the output lh_V1_Juelich_thr50_binarized_voltosurf.nii.gz
(3) Then with that binarized_voltosurf.nii.gz file as the input, I ran the below mri_cor2label command, which gave me the output lh_V1_Juelich_thr50_binarized_voltosurf.label (the label file that won't open)
Thanks!! Steph
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, April 20, 2016 11:13 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label
can you send me the label file?
On 04/20/2016 10:49 AM, DeCross, Stephanie N. wrote: I /think/ it’s really a label file? I took my binarized nii.gz and ran
mri_cor2label -- c NAME.nii.gz -- id 1 -- l ./newname.label
and I was under the impression that this turned it into a label file.
Yes, I get exactly the same errors when I try to open the label in both programs from the command line.
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
On Apr 19, 2016, at 1:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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#Sig... 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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu] Sent: Wednesday, April 13, 2016 5:10 PM To: freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@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.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@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 <lh_V1_Juelich_thr50_binarized.nii.gz><lh_V1_Juelich_thr50_binarized_voltosurf.nii.gz><lh_V1_Juelich_thr50_binarized_voltosurf.label>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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DeCross, Stephanie N. -
Douglas N Greve