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> 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#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-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

--
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