Hi Trisanna
can you run:
head /data-01/trisanna/freesurfer/icbm-102/label/labeltest.label
and send us the output?
cheers
Bruce
On Tue, 19
Apr 2016, 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#Si
gnal[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 Neuroscience
Psychology
On Tue, Apr 19, 2016 at 8:59 PM, Trisanna Sprung-Much
<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. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve
<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
>> <mailto: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
>> > <mailto: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
>> >
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
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>> sent to
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>> > but does not contain patient information, please
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>> > sender and properly
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>> >
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>> >
>> >
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>> > Freesurfer@nmr.mgh.harvard.edu
>> >
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>>
>> --
>> 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:
>>
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>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>>
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>>
>>
>>
>>
>>
>
>
> _______________________________________________
> 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:
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_______________________________________________
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