This program will take the aparc+aseg.nii.gz and
aparc.a2009s+aseg.nii.gz parcellation files produced by FreeSurfer
(FS) and converted to NIFTI by @SUMA_Make_Spec_FS, and make the
following related data sets (with the same prefix) for each:
+ A copy of the whole parcellation/segmentation and renumber the
ROIs to be smaller (for colorbar representation); this file
is called "*_REN_all.nii.gz".
+ Tissue segmentation maps (not binary, but containing the
renumbered ROI values), based on our best guesses of of what
each is, from both the 'mri_binarize' command in FS and our
own supplementary reading of the ROI names. The following
files are output:
*_REN_gm.nii.gz :gray matter
*_REN_wmat.nii.gz :white matter
*_REN_csf.nii.gz :cerebrospinal fluid
*_REN_vent.nii.gz :ventricles and choroid plexus
*_REN_othr.nii.gz :optic chiasm, non-WM-hypointens, etc.
*_REN_unkn.nii.gz :FS-defined "unknown", with voxel value >0
... and, added in Nov, 2019, more dsets for convenience in
afni_proc.py and FATCAT processing:
*_REN_gmrois.nii.gz :gray matter ROIs without '*-Cerebral-Cortex'
dots. This ROI file might be more
useful for tracking or for making
correlation matrices than
*_REN_gm.nii.gz, because it doesn't
include the tiny scattered bits of the
fs_ap_wm.nii.gz :mask (not map!) of WM, excluding the dotted
part from FS. Useful for including in
afni_proc.py for tissue-based regressors.
fs_ap_latvent :mask (not map!) of the lateral ventricles,
'*-Lateral-Ventricle'. Useful for
including in afni_proc.py for
+ A labeltable of the new ROI values: "*_REN_all.niml.lt".
This labeltable is attached to each of the *_REN_*.nii.gz