I am trying to do PVC on FBB-PET images using the following commands:

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mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta 

mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6 --seg gtmseg.mgz --rescale 174 --default-seg-merge  --auto-mask  --mgx .1 --o s_001_pet_fbb

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The problem is that when overlaying the mgx.ctxgm.nii.gz file with the T1.mgz of the corresponding subject, they don't match, since the resulting MG-image is in the space of the original PET (without PVC) instead of in the space of the freesurfer subject.

Marina