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 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-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 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
>> <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
>> >> >
>> >> > --
>> >> > Douglas N. Greve, Ph.D.
>> >> > MGH-NMR Center
>> >> > greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>
>> >> <mailto:greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>>
>> >> > Phone Number: 617-724-2358 <tel:617-724-2358>
>> <tel:617-724-2358 <tel:617-724-2358>>
>> >> > Fax: 617-726-7422 <tel:617-726-7422>
>> <tel:617-726-7422 <tel:617-726-7422>>
>> >> >
>> >> > Bugs:
>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> >> > FileDrop: 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>
>> >> >
>> >>
>> <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>
>> >> <mailto: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
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>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > Freesurfer mailing list
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>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >> >
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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>
>> >> FileDrop: 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
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>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >>
>> >>
>> >>
>> >>
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> <mailto: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 <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>
>> FileDrop: 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/
>>
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>>
>>
>>
>>
>>

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>
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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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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