I wanted just to compute rescaled PET image without any PVC but following the same process as if I would have applied PVC. Moreover, I didn’t want to reduce FOV with auto mask generated (to still be in the gtmseg space). So I ran the following command:

mri_gtmpvc --i PET.lps.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --no-reduce-fov --rbv --o nopvc_nGMcerebpons --threads 4 --rescale 8 47 174

1) However, in the output directory rbv.nii.gz file still had a reduced fov:

          type: nii

    dimensions: 297 x 381 x 363

   voxel sizes: 0.500000, 0.500000, 0.500000

          type: FLOAT (3)

           fov: 148.500

Compared to the gtmseg.mgz:

         type: MGH

    dimensions: 334 x 452 x 424

   voxel sizes: 0.500000, 0.500000, 0.500000

          type: INT (1)

           fov: 226.000

I tried also to remove the —auto-mask option without success. Did I miss something?

2) I wonder why the process took so much time while there is just a rescaling to apply when using --psf 0 --no-tfe?

Best,

Matthieu