You probably set up the FSFAST analysis to sample onto the fsaverage
surface (in your mkanalysis-sess command). There are a couple of things
you can do: 1. redo the FSFAST analysis using "self" instead of
fsaverage. 2. map the beta.nii to the subject's native anatomy using
mri_surf2surf, or 3. Run mri_vol2surf with --trgsubject fsaverge to have
your MRS output in fsaverage space


On 01/09/2018 03:00 PM, Poortata Shirish Lalwani wrote:
> Hello Freesurfer experts,
> We are obtaining MRS data and functional MRI data on two separate days
> for each subject. We use structural scan obtained during both these
> sessions for the freesurfer segmentation.
> MRS scan gives us a binary mask (nii format) in the same space as the
> structural image obtained during that particular scan. We want to use
> this binary mask during the surface based functional MRI analysis.
> I tried the following process to do this:
> 1) Registered the structural image to orig.mgz using:
> bbregister --mov t1spgr.nii --s subject --t1 --init-fsl --reg
> register.dat
> 2) Applied the register.dat created by above process to the binary
> mask to transform it into the orig.mgz space using:
> mri_vol2vol --reg register.dat --mov gabarightxyz_mask.nii --fstarg
> --o gabarightmask.mgh --interp nearest
> (When I overlay this mask on orig.mgz using freeview they appear in
> the correct position.)
> 3) I then converted the volume to surface space using mri_vol2surf.
> mri_vol2surf --src gabarightmask.mgh --out gabarightsurf.nii --srcreg
> myregister.dat --hemi rh
> However the size of this mask created by mri_vol2surf process is
> (145236vertices) different from the size of beta.nii (163842 vertices)
> that is created using selxavg. Is one of the above steps wrong? How to
> resolve this discrepancy?
>
> Best,
> Pia
>
> On Mon, Jan 8, 2018 at 2:58 PM, Poortata Shirish Lalwani
> <poortata@umich.edu <mailto:poortata@umich.edu>> wrote:
>
>     Hi,
>     We are obtaining MRS data and functional MRI data on two separate
>     days for each subject. We use structural scan obtained during both
>     these sessions for the freesurfer segmentation. MRS scan gives us
>     a binary mask (nii format) in the same space as the structural
>     image obtained during that particular scan. We want to use this
>     binary mask during the surface based functional MRI analysis. I am
>     not sure how to transform this binary mask to the surface space.
>     Is there a way to do this?
>
>     Best,
>     Pia
>
>
>
>
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> 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
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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