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 <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. CandidateMcGill University
Integrated Program in Neuroscience
Psychology
On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve <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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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