Hi Doug and Bruce *This what I get when I run the head command on the label:*
trisanna@kaplan:~$ head /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label #!ascii label , from subject lh.pial vox2ras=TkReg 1651 -1 -29437.500 -0.500 0.500 0.0000000000 -1 -30660.500 -0.500 0.500 0.0000000000 -1 -30675.500 -0.500 0.500 0.0000000000 -1 -30676.500 -0.500 0.500 0.0000000000 -1 -30748.500 -0.500 0.500 0.0000000000 -1 -30760.500 -0.500 0.500 0.0000000000 -1 -30798.500 -0.500 0.500 0.0000000000 -1 -30815.500 -0.500 0.500 0.0000000000 *When I re-run freeview without the space you pointed out, I get the following:* trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/labeltest.label *** Error in `freeview.bin': double free or corruption (out): 0x0000000028604a50 *** Abort (core dumped) *If I try an already exiting label in the terminal, it works perfectly:* trisanna@kaplan:~$ freeview -f /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=/data-01/trisanna/freesurfer/icbm-102/label/lh.BA44.label best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Apr 19, 2016 at 11:11 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Can you load another label, eg, lh.cortex.label? Also, I noticed that > there is a space between "label=" and "/data/..." in the command line > below. That space should not be there, so if it was there when you ran the > command try again without the space. > > > On 4/19/16 9:19 PM, Trisanna Sprung-Much wrote: > > Hi Doug > > I tried again in the terminal and got this: > > * trisanna@kaplan:~$ freeview -f > /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label= > /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label * > [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 kaplan by trisanna Tue > Apr 19 21:13:58 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 > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much < > <trisanna.sprung-m...@mail.mcgill.ca>trisanna.sprung-m...@mail.mcgill.ca> > wrote: > >> Hi Doug >> >> I thought this was the case as well but when I try manually in Freeview >> and select the correct label, Freeview crashes and gives this error in the >> terminal: >> >> trisanna@kaplan:~$ freeview >> *** Error in `freeview.bin': double free or corruption (out): >> 0x0000000029080920 *** >> Abort (core dumped) >> >> >> -- >> Ph.D. Candidate >> McGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve < >> <gr...@nmr.mgh.harvard.edu>gr...@nmr.mgh.harvard.edu> wrote: >> >>> I don't think that is the problem. The problem is that it cannot find >>> the file. Try giving it the whole path >>> >>> On 04/19/2016 05:45 PM, Bruce Fischl wrote: >>> > Hi Trisanna >>> > >>> > if your output is .mgz it isn't a label file. Labels are stored in >>> > .label names and are text files. The .mgz is a scalar field over the >>> > surface (that is, a vector with a single value at each surface >>> > location). In freeview you can view it as: >>> > >>> > freeview -f lh.inflated:overlay=surfaceoverlay.mgz >>> > >>> > >>> > cheers >>> > Bruce >>> > >>> > On Tue, 19 Apr 2016, Trisanna Sprung-Much wrote: >>> > >>> >> Hi Doug >>> >> >>> >> So I ran mri_vol2surf and generated my .mgz surface overlay using >>> >> --regheader as you suggested. I than ran mri_cor2label using that >>> >> .mgz file. >>> >> This also completed successfully. However, when I then try to open >>> >> the pial >>> >> surface and the corresponding new label in freeview, it says it >>> >> cannot read >>> >> the label. Below is what I ran. I tried the same thing for the >>> inflated >>> >> surface. >>> >> >>> >> I put labelid as "1" as I was unsure as to what to put. Could this >>> have >>> >> affected the label creation? >>> >> >>> >> Trisanna >>> >> >>> >> >>> >> trisanna@kaplan:~$ mri_vol2surf --mov >>> >> /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc --o >>> >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --regheader >>> >> icbm-102 --hemi lh --surf pial >>> >> srcvol = /data-01/trisanna/freesurfer/icbm-102/mri/labels5.mnc >>> >> srcreg unspecified >>> >> srcregold = 0 >>> >> srcwarp unspecified >>> >> surf = pial >>> >> hemi = lh >>> >> reshape = 0 >>> >> interp = nearest >>> >> float2int = round >>> >> GetProjMax = 0 >>> >> INFO: float2int code = 0 >>> >> INFO: changing type to float >>> >> Done loading volume >>> >> Computing registration from header. >>> >> Using /data-01/trisanna/freesurfer/icbm-102/mri/orig.mgz as target >>> >> reference. >>> >> Reading surface /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial >>> >> Done reading source surface >>> >> Mapping Source Volume onto Source Subject Surface >>> >> 1 0 0 0 >>> >> using old >>> >> Done mapping volume to surface >>> >> Number of source voxels hit = 85413 >>> >> Writing to /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >>> >> Dim: 169941 1 1 >>> >> >>> >> >>> >> trisanna@kaplan:~$ mri_cor2label --i >>> >> /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz --id 1 --l >>> >> /data-01/trisanna/freesurfer/icbm-102/label/labeltest --surf lh.pial >>> >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >>> >> Loading mri /data-01/trisanna/freesurfer/icbm-102/surfaceoverlay.mgz >>> >> ------- Vox2RAS of input volume ----------- >>> >> -1.000 0.000 0.000 84970.500; >>> >> 0.000 0.000 1.000 -0.500; >>> >> 0.000 -1.000 0.000 0.500; >>> >> 0.000 0.000 0.000 1.000; >>> >> Scanning the volume >>> >> Found 1651 label voxels >>> >> Writing label file >>> /data-01/trisanna/freesurfer/icbm-102/label/labeltest >>> >> Centroid: -56170.34 -0.50 0.50 >>> >> mri_cor2label completed SUCCESSFULLY >>> >> >>> >> >>> >> trisanna@kaplan:~$ freeview -f >>> >> /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial:label=labeltest >>> >> No such file or directory >>> >> freeview.bin: could not open label file labeltest.label >>> >> No such file or directory >>> >> LabelRead failedNo such file or directory >>> >> en label file labeltest.label >>> >> >>> >> >>> >> >>> >> -- >>> >> Ph.D. CandidateMcGill University >>> >> Integrated Program in Neuroscience >>> >> Psychology >>> >> >>> >> >>> >> On Tue, Apr 19, 2016 at 4:15 PM, Trisanna Sprung-Much >>> >> <trisanna.sprung-m...@mail.mcgill.ca> wrote: >>> >> many thanks - will give this a go! >>> >> >>> >> -- >>> >> Ph.D. CandidateMcGill University >>> >> Integrated Program in Neuroscience >>> >> Psychology >>> >> >>> >> >>> >> On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve >>> >> <gr...@nmr.mgh.harvard.edu> wrote: >>> >> yes, but the surface overlay is in mgz (or nii.gz) format >>> >> >>> >> On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote: >>> >> > Hi Doug >>> >> > >>> >> > below is the email I had written last Friday. I thought >>> >> it got lost in >>> >> > the mix. I was told by Bruce to use identity.nofile as >>> >> the >>> >> > transformation since my labels and T1s are already in >>> >> the same space >>> >> > and I just want to resample my labels to the surfaces. >>> >> > >>> >> > *I will try, as you suggest, --regheader * >>> >> > >>> >> > When I do "mri_cor2label --help" it says it uses surface >>> >> overlays or >>> >> > volumes. *I am not sure why I want to generate a volume >>> >> with >>> >> > mri_vol2surf* - shouldn't I generate a surface overlay >>> >> that I can then >>> >> > create as a label using mri_cor2label? >>> >> > >>> >> > many thanks >>> >> > >>> >> > Trisanna >>> >> > >>> >> > >>> >> > >>> >> > thanks Bruce >>> >> > >>> >> > I could not find identity.nofile anywhere, when I ran >>> >> mri_vol2surf I >>> >> > got the following error >>> >> > >>> >> > trisanna@kaplan:~$ mri_vol2surf --mov >>> >> > /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >>> >> --o >>> >> > /data-01/trisanna/freesurfer/icbm-112 --reg >>> >> identity.nofile --hemi lh >>> >> > srcvol = >>> >> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz >>> >> > srcreg = identity.nofile >>> >> > srcregold = 0 >>> >> > srcwarp unspecified >>> >> > surf = white >>> >> > hemi = lh >>> >> > reshape = 0 >>> >> > interp = nearest >>> >> > float2int = round >>> >> > GetProjMax = 0 >>> >> > INFO: float2int code = 0 >>> >> > INFO: changing type to float >>> >> > Done loading volume >>> >> > regio_read_register(): No such file or directory >>> >> > Could not open identity.nofile >>> >> > >>> >> > >>> >> > >>> >> > On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl >>> >> > < <fis...@nmr.mgh.harvard.edu>fis...@nmr.mgh.harvard.edu >>> >> <mailto: <fis...@nmr.mgh.harvard.edu>fis...@nmr.mgh.harvard.edu>> >>> wrote: >>> >> > Hi Trisanna >>> >> > >>> >> > you can give the transformation "file" named >>> >> identity.nofile and it >>> >> > will assume that the transform is the identity. You can >>> >> then use >>> >> > mri_vol2label to sample the label onto the surface and >>> >> visualize it with: >>> >> > >>> >> > freeview -f lh.inflated:label=lh.labels.label >>> >> > >>> >> > or some such >>> >> > >>> >> > cheers >>> >> > Bruce >>> >> > >>> >> > On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote: >>> >> > >>> >> > Hi there >>> >> > >>> >> > Just to reiterate my point above, when I open a surface >>> >> created in >>> >> > Freesurfer with my labels.mgz (converted from minc) in >>> >> Freeview (i.e. no >>> >> > transformations have been performed) I get the following >>> >> snapshot >>> >> > #1. Clearly, my original labels are aligned with the >>> >> surface, as they >>> >> > should >>> >> > be since Freesurfer did not alter the space. So, how can >>> >> I use mrivol2surf >>> >> > to resample the surface such that the vertices carry the >>> >> label info? What >>> >> > output format should I use in mrivol2surf? How can I >>> >> open this output in >>> >> > Freeview? >>> >> > >>> >> > For instance, when I try a .dat that creates no >>> >> transformation and >>> >> > save the >>> >> > output as .mgz and use Overlay in Freeview, I get >>> >> snapshot #2. So, >>> >> > something >>> >> > is going wrong in my mrivol2surf command. >>> >> > >>> >> > My apologies for the questions >>> >> > Trisanna >>> >> > >>> >> > >>> >> > >>> >> > -- >>> >> > Ph.D. Candidate >>> >> > McGill University >>> >> > Integrated Program in Neuroscience >>> >> > Psychology >>> >> > >>> >> > >>> >> > On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve >>> >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> >>> >> wrote: >>> >> > >>> >> > I'm not sure what identity.nofile is or what you are >>> >> trying to do (no >>> >> > previous info in the email). If whatever you are trying to >>> >> map to the >>> >> > surface is already in anatomical space (so no registration >>> >> necessary), >>> >> > then you can use --regheader with mri_vol2surf. >>> >> mri_cor2label will >>> >> > take >>> >> > a volume format as input (ie, mgz, nii.gz ,etc) >>> >> > >>> >> > On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote: >>> >> > > >>> >> > > Hi All! >>> >> > > >>> >> > > Could someone please tell me how to run mri_vol2surf >>> >> using >>> >> > > identity.nofile as the transformation? I cannot find any >>> >> > documentation >>> >> > > on identity.nofile >>> >> > > >>> >> > > Additionally, if my next step is to use the output of >>> >> > mri_vol2surf in >>> >> > > mri_cor2label, which takes surface overlays OR volumes, >>> >> what format >>> >> > > should my output be for mri_vol2surf? >>> >> > > >>> >> > > many thanks! >>> >> > > >>> >> > > Trisanna >>> >> > > >>> >> > > -- >>> >> > > Ph.D. Candidate >>> >> > > McGill University >>> >> > > Integrated Program in Neuroscience >>> >> > > Psychology >>> >> > > >>> >> > > >>> >> > > >>> >> > > _______________________________________________ >>> >> > > Freesurfer mailing list >>> >> > > <Freesurfer@nmr.mgh.harvard.edu> >>> Freesurfer@nmr.mgh.harvard.edu >>> >> > <mailto: <Freesurfer@nmr.mgh.harvard.edu> >>> 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 >>> >> <mailto:gr...@nmr.mgh.harvard.edu> >>> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >>> >> > Fax: 617-726-7422 <tel:617-726-7422> >>> >> > >>> >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> >> > FileDrop: <https://gate.nmr.mgh.harvard.edu/filedrop2> >>> https://gate.nmr.mgh.harvard.edu/filedrop2 >>> >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >> > >>> >> <http://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 >>> >> <mailto: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. >>> >> > >>> >> > >>> >> > >>> >> > >>> >> > _______________________________________________ >>> >> > 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 >>> >> >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > 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. > >
_______________________________________________ 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.
