AFNI program: @SUMA_renumber_FS
Output of -help
This script is now run at the end of modern @SUMA_Make_Spec_FS
commands, or it can be run separately for data that had been
processed using older versions of AFNI.
Originally written and tested on FreeSurfer (FS) v5.3 output from
default running of 'recon-all'. This should now work for FS v6.0
default running of 'recon-all', as well.
Written by PA Taylor (NIMH, NIH; 2016-7).
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
At the moment, the function just takes a single, required
argument, which is the location of the 'SUMA/' directory created
by @SUMA_Make_Spec_FS. The program also requires being able to
see the two 'afni_fs_aparc+aseg_*.txt' files in the AFNI binary
directory: that is where the information on renumbering the FS
$ @SUMA_renumber_FS SUMA_DIR
where SUMA_DIR is either the full or relative path to the 'SUMA/'
directory (including that directory name).
But again, note that this program will mainly just be run by
$ @SUMA_renumber_FS /data/study/SUBJ_01/FS/SUMA
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Wed Jul 28 19:40:52 EDT 2021