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Alright, thanks I confused that. I already found a better way for my purposes. Im just running mri_gtmpvc using the flags —psf=0 and —no-tfe to get the non PVC subcortical SUVs.

Am 17.05.2019 um 17:28 schrieb Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>:
In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz --ctab-default ...
when you use --annot, you are saying that the input is on the surface.

On 5/17/2019 9:07 AM, Boris Rauchmann wrote:
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Dear Freesurfer community,

I am trying to extract SUV values from sub-cortical segmentation or gtmseg I don t want to use any PVC.

I used the following commands:

gtmseg --s xyz

then

mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta

following

mri_vol2vol --mov abetapet.nii --reg abetapet.reg.lta --targ orig.mgz --o abetapet.sm00.nii.gz
and

mri_segstats --annot xyz lh gtmseg --i abetapet.sm00.nii.gz --sum xyz_abeta.stats

resulting in this dimension mismatch error:

input 256 256 256
seg 416 450 476

Is that the correct way for doing this analysis? any suggestions how to solve the mismatch error?

Thanks,

Boris
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