On 2/16/19 2:54 PM, Matthieu Vanhoutte wrote:

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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

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