thanks Bruce
trisanna@kaplan:~$ mri_vol2surf --mov /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh
srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
srcreg = identity.nofile
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): No such file or directory
Could not open identity.nofile
On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Trisanna
you can give the transformation "file" named identity.nofile and it will assume that the transform is the identity. You can then use mri_vol2label to sample the label onto the surface and visualize it with:
freeview -f lh.inflated:label=lh.labels.label
or some such
cheers
Bruce
On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
Hi there
Just to reiterate my point above, when I open a surface created in
Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no
transformations have been performed) I get the following snapshot
#1. Clearly, my original labels are aligned with the surface, as they should
be since Freesurfer did not alter the space. So, how can I use mrivol2surf
to resample the surface such that the vertices carry the label info? What
output format should I use in mrivol2surf? How can I open this output in
Freeview?
For instance, when I try a .dat that creates no transformation and save the
output as .mgz and use Overlay in Freeview, I get snapshot #2. So, something
is going wrong in my mrivol2surf command.
My apologies for the questions
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> 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
greve@nmr.mgh.harvard.edu
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