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
- 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?
- 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