It may be that the registration is off. You should load your gm volume with the surfaces on top, something like
tkmeditfv -f orig.mgz -aux gm_values2anat.nii -surfs
On 12/06/2016 01:41 PM, Ilaria Mazzonetto wrote:
Hi Freesurfer User,
I would like to map a volume to a surface. I have a T1 image (SubjX) with resolution 1x1x1 and a gray matter mask with resolution 6x6x6. The voxels in the lower resolution image (gm_values.nii) have zero value if they are not in the gray matter and a value between 0.1 and 20 if they are in the gray matter. What I want to do is mapping this values in the pial surface. I runned recon-all with T1 image and I coregistered the lower resolution image (the mask) to higher resolution image with FSL (gm_values2anat.nii). Then I runned mri_vol2surf -- src gm_values2anat.nii --regheader SubjX --hemi lh --surf pial --o gm_values_lhsurf.mgh. I do not understand what the options for surface normal projection mean. I inspected the result with tksurfer, setting fminmask 0 20, and there are a lot of holes.
Do you think there is something wrong in what I did?
Any help would be greatly appreciated.
Regards.
Ilaria
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