Hi,
Thank you for your answer.
I am using
@SSwarper -input $subject.$session.anat+orig.BRIK -base /Users/ramotlab/abin/MNI152_2009_template_SSW.nii.gz -subid $subject.$session.$scan.SE
and afterward the proc.py commands including anat_follower_ROI.
The problem is that I am trying to get a gray matter mask in MNI (cortex+subregions) extracted from freesurfer parcellation aparc+aseg and the transformation is not going well.
I tried:
to create the gray matter mask:
mri_binarize --i aparc+aseg.s1.mgz --gm --o GMmask.s1.mgz
to convert the mgz file to nii:
mri_convert GMmask.s1.mgz GMmask.s1.nii
to transform grom nii to afni format:
3dcopy GMmask.s1.nii GMmask.s1.use
to use the transformation matrix from @SSwarper conducted for proc.py to transform the mask to MNI:
3dNwarpApply -nwarp 'anatQQ.sub1.s1.movie1.SE_WARP.nii anatQQ.sub1.s1.movie1.SE.aff12.1D' -source GMmask.s1.use+orig
It comes out in orig and with no alignment to the anat data.
