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. CandidateMcGill University
Integrated Program in NeurosciencePsychology
On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca> wrote:
Hi DougI 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. CandidateMcGill University
Integrated Program in NeurosciencePsychology
On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve <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> 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
>> <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>>
>> 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
>> > >
>> > >
>> > >
>> > > _______________________________________________
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>> > >
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>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > greve@nmr.mgh.harvard.edu
>> <mailto:greve@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>
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>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> >
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>> >
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>> >
>> 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
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>> > contains patient information, please contact the Partners
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>> --
>> 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
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>>
>>
>
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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