I am working on running some scans through FreeSurfer. I have scans at both 0.5mm and 0.8mm that have all been skull stripped and N3 corrected. The images have good contrast in general and specifically are fairly good in the subcortical regions. I am skipping a bunch of the FreeSurfer pipeline and bringing my scans directly into the mri_normalize step. I have been running it with the -monkey option and a set of about 25 to 50 control points in various areas of white matter. The normalization yields very good contrast in cortex, but basically removes any sign of gray matter in the sub cortical region (e.g. it basically all winds up with a value of 110). Is there any way to combat this problem?
-Eric _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
