Re: [Freesurfer] Issue with vol2surf

It is just mri_vol2surf like you have using the --regheader

On 5/15/19 4:53 PM, Martin Juneja wrote:

External Email - Use Caution

Thanks Doug, sure I will try that. Would you mind sharing the command line to sample ROIs onto MNI surface (after running recon-all on MNI template)?

On Wed, May 15, 2019 at 1:32 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:

I would run recon-all on the MNI152, then sample the ROIs onto the
MNI152 surface, then transfer them to fsaverage using
mris_apply_reg or
mri_surf2surf.

On 5/15/19 1:46 PM, Martin Juneja wrote:
>
>         External Email - Use Caution
>
> Hi FS experts,
>
> I am interested in displaying my ROI: ROI.nii (which is in standard
> space: avg152T1.nii.gz) on to fsaverage space. For that, I
performed
> following steps:
>
> (1). Registered my template to fsaverage and saved the
transformation
> matrix TT.dat as following:
>
> fslregister --s fsaverage --mov ROIs/avg152T1.nii.gz --reg TT.dat
>
>
> (2). Mapped my ROI to fsaverage using the transformation matrix
TT.dat
> as following:
>
> mri_vol2surf --mov ROIs/ROI.nii --reg TT.dat --projdist-max 0 1 0.1
> --interp nearest --hemi lh --out ROIs/ROI_Trans.mgh
>
>
> This works for 12 out of my 14 ROIs, but two of the ROIs are not
> displaying properly, and after the transformation when I displayed
> those on fsaverage space, these ROIs cover the whole hemisphere
> (please see attached: e.g. overlaying an ROI_Trans on fsvaerage
space).
>
>
> I confirmed that both of these (non-working) ROIs (in .nii form)
look
> fine on avg152T1.nii.gz, and on fsaverage when applying the
> transformation as following:
>
> tkmedit fsaverage T1.mgz -overlay ROIs/ROI.nii -overlay-reg TT.dat
> -fthresh 0.5 -surface lh.white -aux-surface lh.white
>
>
> I would really appreciate any help.
>
>
> Thanks.
>
>
>
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