There is not an easy way to do this yet. If you have your segmentations in the conformed anatomical space, you can merge them with gtmseg.mgz with something like mri_vol2vol --interp nearest --mov yoursegs.mgz --targ gtmseg.mgz --o yoursegs-in-gtmseg-space.mgz mergeseg --src gtmseg.mgz --merge yoursegs-in-gtmseg-space.mgz --o gtmseg+yoursegs.mgz You will then need to copy gtmseg.ctab to gtmseg+yoursegs.ctab and edit it to include your new segs. Note that your new seg numbers should not overlap with anything in gtmseg. Once you create the new ctab, you can just copy it to other subjects. Finally, copy gtmseg.lta to gtmseg+yoursegs.lta Then run mri_gtmpvc passing --seg gtmseg+yoursegs.mgz

On 10/29/2023 1:21 PM, Dawn Matthews wrote:

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Congratulations to the FreeSurfer team in the continued progress made in the FS tool set.  I wondered if you could comment on whether it is feasible to create a custom reference region (other than specifying, for example, cerebellar cortex or another predefined FS mask) for PETsurfer kinetic modeling (e.g. a cerebellum subfield) or whether there perhaps is an existing cerebellar subfield atlas that can be run with PETSurfer (e.g. crus2)?  In addition, can you please confirm whether the Logan model can be run using a reference region (i.e. without requiring arterial input)?  Thanks very much and kind regards.

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