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Dear Freesurfer Experts,
I am interested in generating a volumetric segmentation and parcellation of the
HCP-MMP1 atlas using mri_surf2volseg - and I have previously done this like so:
mri_surf2volseg --o $sub/HCP-MMP1_fsSpace.mgz \
--label-cortex --i $sub/mri/aseg.mgz --threads 4 \
--lh-annot $sub/label/lh.HCP-MMP1.annot 1000
--lh-cortex-mask $sub/label/lh.cortex.label \
--lh-white $sub/surf/lh.white --lh-pial
$sub/surf/lh.pial \
--rh-annot $sub/label/rh.HCP-MMP1.annot 2000
--rh-cortex-mask $sub/label/rh.cortex.label \
--rh-white $sub/surf/rh.white --rh-pial
$sub/surf/rh.pial
However rather than use the regular white matter surface generated by recon-all
(as above), I want to parcellate between the pial surface and a superficial
white matter surface 1mm below the GM/WM boundary.
I have generated this superficial white matter (SWM) surface for both
hemispheres like so:
mris_expand lh.white -1 lh.SWM.1mm
My first though was just to replace the --rh-white / --lh-white inputs with the
SWM surface, but after running this, the output remains the same.
I think I may also need use a different input than aseg.mgz, but not sure what
this would be or how to generate it.
Any assistance you could offer with the would be greatly appreciated.
Many thanks,
George
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