[Freesurfer] Separating Specific Areas from a .nii.gz file

Dear life savers, headache relievers and brain science dreamers,

PROLOG: I'm trying to separate out some regions from a .nii.gz file. I start with a surface parcellation in .annot (Freesurfer land) that I convert to EXAMPLE.nii.gz using mri_aparc2aseg.

THE GOAL: To get a .nii.gz file for each one of these regions. Using fslmaths, I threshold the EXAMPLE.nii.gz file above & below the intensity of that region & save as REGION_name.nii.gz.

THE PROBLEM: This method is working for the majority of the regions. But many of the output REGION_name.nii.gz files are completely empty. They are there in the original EXAMPLE.nii.gz but are lost in the thresholding some(how/where).

THE SOLUTION: Your kind reply...

Thanks very much. -Sam