Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

thanks, Doug! sorry, I had misinterpreted the --surf argument when I had
originally checked --help. Got the proper label created AND got the
overlay.mgz to work as well. All my labels are there in the overlay.mgz
created using mri_vol2surf once I change the thresholds of the overlay - I
can then isolate a particular label by creating a .label. am SUPER
pleased Thank you so much :)

Out of curiosity, is there any particular reason why I should be using an
overlay.mgz versus a .label text file?

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Apr 20, 2016 at 12:00 PM, Douglas N Greve  wrote:

> nope, you need to give it just the name of the subject and the
> hemisphere. Run it with --help for more info
>
> On 04/20/2016 11:35 AM, Trisanna Sprung-Much wrote:
> > 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   -0.500.50
> > 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
> > mailto:gr...@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 0.00
> > > -1  -30660.500  -0.500  0.500 0.00
> > > -1  -30675.500  -0.500  0.500 0.00
> > > -1  -30676.500  -0.500  0.500 0.00
> > > -1  -30748.500  -0.500  0.500 0.00
> > > -1  -30760.500  -0.500  0.500 0.00
> > > -1  -30798.500  -0.500  0.500 0.00
> > > -1  -30815.500  -0.500  0.500 0.00
> > >
> > >
> > > *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):
> > > 0x28604a50 ***
> > > 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
> > > mailto:gr...@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]P

Re: [Freesurfer] identity.nofile

[Douglas N Greve]

nope, you need to give it just the name of the subject and the 
hemisphere. Run it with --help for more info

On 04/20/2016 11:35 AM, Trisanna Sprung-Much wrote:
> 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   -0.500.50
> 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 
> mailto:gr...@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 0.00
> > -1  -30660.500  -0.500  0.500 0.00
> > -1  -30675.500  -0.500  0.500 0.00
> > -1  -30676.500  -0.500  0.500 0.00
> > -1  -30748.500  -0.500  0.500 0.00
> > -1  -30760.500  -0.500  0.500 0.00
> > -1  -30798.500  -0.500  0.500 0.00
> > -1  -30815.500  -0.500  0.500 0.00
> >
> >
> > *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):
> > 0x28604a50 ***
> > 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
> > mailto:gr...@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
> >> 

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

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   -0.500.50
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  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 0.00
> > -1  -30660.500  -0.500  0.500 0.00
> > -1  -30675.500  -0.500  0.500 0.00
> > -1  -30676.500  -0.500  0.500 0.00
> > -1  -30748.500  -0.500  0.500 0.00
> > -1  -30760.500  -0.500  0.500 0.00
> > -1  -30798.500  -0.500  0.500 0.00
> > -1  -30815.500  -0.500  0.500 0.00
> >
> >
> > *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):
> > 0x28604a50 ***
> > 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
> > mailto:gr...@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 

Re: [Freesurfer] identity.nofile

[Douglas N Greve]

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 0.00
> -1  -30660.500  -0.500  0.500 0.00
> -1  -30675.500  -0.500  0.500 0.00
> -1  -30676.500  -0.500  0.500 0.00
> -1  -30748.500  -0.500  0.500 0.00
> -1  -30760.500  -0.500  0.500 0.00
> -1  -30798.500  -0.500  0.500 0.00
> -1  -30815.500  -0.500  0.500 0.00
>
>
> *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): 
> 0x28604a50 ***
> 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 
> mailto:gr...@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
>> > > wrote:

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

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 0.00
-1  -30660.500  -0.500  0.500 0.00
-1  -30675.500  -0.500  0.500 0.00
-1  -30676.500  -0.500  0.500 0.00
-1  -30748.500  -0.500  0.500 0.00
-1  -30760.500  -0.500  0.500 0.00
-1  -30798.500  -0.500  0.500 0.00
-1  -30815.500  -0.500  0.500 0.00


*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):
0x28604a50 ***
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 
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-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):
>> 0x29080920 ***
>> 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 <
>> 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 

Re: [Freesurfer] identity.nofile

[Douglas Greve]

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 
> 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):
0x29080920 ***
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
mailto: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 -

Re: [Freesurfer] identity.nofile

[Bruce Fischl]

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
 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):
0x29080920 ***
Abort (core dumped)


--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve
 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: cha

Re: [Freesurfer] identity.nofile

[Bruce Fischl]

Hi Trisanna

your output is a .mgz file, which is *not* a label. Try loading it as an 
overlay. The label format is different (ascii for one thing, and only part 
of the surface for another).


cheers
Bruce

On Tue, 19 Apr 2016, Trisanna Sprung-Much 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):
0x29080920 ***
Abort (core dumped)


--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 6:17 PM, Douglas N Greve 
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
  >>  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
  >>  wrote:
  >>   

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

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-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):
> 0x29080920 ***
> 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 <
> 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 So

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

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):
0x29080920 ***
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 
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   -0.500.50
> >> 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
> >>  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
> >>  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 

Re: [Freesurfer] identity.nofile

[Douglas N Greve]

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   -0.500.50
>> 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
>>  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
>>  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
>>   > src

Re: [Freesurfer] identity.nofile

[Bruce Fischl]

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
 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
 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
  > mailto:fis...@nmr.mgh.harvard.edu>> wrote:
  > Hi Trisanna
  >
  > you can give the transformation "file" named
 

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

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   -0.500.50
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. Candidate
McGill 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. Candidate
> McGill 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
>> > 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.

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

many thanks - will give this a go!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 3:48 PM, Douglas N Greve 
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
> > 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
> > 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
> > 
> > > 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.harvar

Re: [Freesurfer] identity.nofile

[Douglas N Greve]

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 
> 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 
> 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
> 
> > 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:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

Re: [Freesurfer] identity.nofile

[Bruce Fischl]

sorry for the confusion. Some of our tools use identity.nofile, but these 
use --regheader


cheers
Bruce

On Tue, 19 Apr 2016, 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[cleardot.gif]



On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl 
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. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve 
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
> 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:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
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 e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.

Re: [Freesurfer] identity.nofile

[Trisanna Sprung-Much]

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 
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 
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
> > 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: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> 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 e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
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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

Re: [Freesurfer] identity.nofile

[Douglas N Greve]

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
> 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: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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 e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] identity.nofile

[Trisanna Sprung-Much]

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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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 e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.