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. < dgr...@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. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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