Hi Doug
I had run mri_cor2label using the --surf option. Is what I did below correct?
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
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 20, 2016 at 11:18 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
I think the problem is that this is being interpreted as a volume label. The first column is the surface vertex number which you can see is all -1s indicating no vertex. To create a surface label, run mri_cor2label with the --surf subject hemi option. Ruopeng, can you add something to freeview to handle this case more elegantly? doug
On 04/20/2016 10:42 AM, Trisanna Sprung-Much wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 seehttp://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 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-much@mail.mcgill.ca <mailto:trisanna.sprung-much@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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-much@mail.mcgill.ca <mailto:trisanna.sprung-much@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 >> <greve@nmr.mgh.harvard.edu <mailto:greve@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 >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@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 >> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> >> wrote: >> > >> > I'm not sure what identity.nofile is or what youare
>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> > > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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