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:
External Email - Use Caution
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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