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 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#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.catrisanna.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.edugreve@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 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 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>fischl@nmr.mgh.harvard.edu <mailto: <fischl@nmr.mgh.harvard.edu>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>
wrote:
I'm not sure what identity.nofile is or what you aretrying to do (no
previous info in the email). If whatever you are trying tomap to the
surface is already in anatomical space (so no registrationnecessary),
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_vol2surfusing
> 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
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