On 2/16/19 2:54 PM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > Dear Douglas, > > 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 Try adding --no-mask_rbv_to_brain > > 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? It does not know that it is only applying a scaling. It is going through the entire process > > Best, > Matthieu > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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