I suspect the problem is with the aseg.mgz input. You can regenerate that with the new surfs with a different call to mri_surf2volseg. However, that will take a --fix-presurf-with-ribbon argument, so you will also have to regenerate the ribbon.mgz file for the new surfaces with mris_volmask

On 1/9/2024 7:23 AM, Thomas, George wrote:

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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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