Hello, 

I am interested in the cortical parcellations at the pial (grey matter) and white matter layers

I have extracted grey matter (pial) and white matter (white) labels for a gyrus (right superior frontal gyrus, label 2028)

mri_annotation2label --subject s1/12copy --hemi rh --labelbase ./12copy/label/rh.cortex --surface pial

mri_annotation2label --subject s1/12copy --hemi rh --labelbase ./12copy/label/rh.cortex --surface white

then converted the above 2 files (renamed to ...-wm and ...-gm) for the superior frontal gyrus  to nifti's for viewing in other applications

mri_label2vol --label ./label/rh.cortex-028.label --o rh-cortex-028-rsfg-wm.nii --identity --temp ./mri/T1.mgz

mri_label2vol --label ./label/rh.cortex-028.label --o rh-cortex-028-rsfg-gm.nii --identity --temp ./mri/T1.mgz

My goal is to run some statistics on 2 nifti's, which requires continuity in the nonzero voxels, in at least 1 of the 3 directions (x/y/z). This isn't the case for this gyri, particularly at the pial layer (shown in blue in the attachment). Is there a way in which this could be achieved? Have I missed any steps? 

Many thanks in advance.

Shads