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):
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
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>> > >
>> 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>
>> >
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>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> >
>>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> > Outgoing:
>> >
>>
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
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>> >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the
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>> > addressed. If you believe this e-mail was sent to you
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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
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>>
>>
>>
>
>
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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
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