Hi, Maya-

There are a couple ways to get this info.

To see the labeltable in an ROI file that has them (and those *REN* files have 'em), you can run:

3dinfo -labeltable aparc.a2009s+aseg_REN_gmrois.nii.gz

In your AFNI binaries directory, you can also see the files used to create those labels, which are called:

afni_fs_aparc+aseg_2000.txt
afni_fs_aparc+aseg_2009.txt

The numbers match the respective output names.

In tcsh you could do:

set aa = `which afni`
cat ${aa:h}/afni_fs_aparc+aseg_2009.txt

... for example.

I think the cerebellum values in the full atlas are:

# FS_NUM  STRING_LABEL                         TISS__TYPE  REN_VAL    COLOR_LUT
7         Left-Cerebellum-White-Matter         tiss__wmat        5    220 248 164 0
8         Left-Cerebellum-Cortex               tiss__gm          6    230 148 34  0
46        Right-Cerebellum-White-Matter        tiss__wmat       25    220 248 164 0
47        Right-Cerebellum-Cortex              tiss__gm         26    230 148 34  0

Only the GM ones will be in the *REN_gmrois* one, so you just need to excise ROI #6 and 26. You could do this with 3dcalc in different ways; one is to use the full dataset and subtract away the ROIs you don't want, which seems useful here since it is a short list:

3dcalc \
    -a aparc.a2009s+aseg_REN_gmrois.nii.gz \
    -b aparc.a2009s+aseg_REN_gmrois.nii.gz"<Left-Cerebellum-Cortex,Right-Cerebellum-Cortex>" \
    -expr 'a-b' \
   -prefix aparc.a2009s+aseg_REN_gmrois_CORT.nii.gz

If you are only excising some integer values and not renumbering otherwise, you can reattach the original labeltable. To reattach a labeltable and integer-valued colormap (for looking at it in the AFNI GUI) afterward, you can:

3drefit -copytables aparc.a2009s+aseg_REN_gmrois.nii.gz aparc.a2009s+aseg_REN_gmrois_CORT.nii.gz
3drefit -cmap INT_CMAP aparc.a2009s+aseg_REN_gmrois_CORT.nii.gz

These are often convenient to do.

--pt



Edited 1 time(s). Last edit at 11/25/2022 10:12AM by ptaylor.