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 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
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