The MGX method is only valid in voxels that have some gray matter in them (defined as 1% in the command line below), so any WM is set to 0 (probably accounts for the big hole that you see). The mgx output is divided into cortical GM and subcortical GM, so you are probably looking at the cortical GM part.
On 10/31/19 1:12 PM, Mackenzie Leigh Carlson wrote: > > External Email - Use Caution > > Hello, > > Wondering if anyone has had issues with PETsurfer partial volume > correction. When I have used it, there are large 'holes' in the white > matter. I am mostly interested in the hippocampal area, which seems > unaffected by these holes, but I'm not sure if I should trust the > outcome enough to still use PVC maps for the hippocampus! Any help is > appreciated. Thank you! > > I am running this: > mri_gtmpvc --i SUV-30-60-float-FixedSlope.nii.gz --reg SUVtoFS.reg.lta > --psf 5 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 > --mgx .01 --o gtmpvc.output.nopons --no-rescale > > > -- > Mackenzie L. Carlson > PhD Candidate in Bioengineering | Stanford University > BA Engineering Sciences | Dartmouth College > (218) 269-7473 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
