This script is used to get labels associated with FreeSurfer’s parcellation and annotation files.
Return the name of an integer labeled area in FreeSurfer’s parcellation. Lookup is based on your installed FreeSurferColorLUT.txt Example:
@FS_roi_label 2180
or
Return the name of an integer labeled area in FreeSurfer’s parcellation Example:
@FS_roi_label -lab 2180
or
Return the name of ranked integer labeled area from the output of 3dRank or 3dmerge -1rank on a FreeSurfer parcellation file. Example:
- @FS_roi_label -rank 198
-rankmap SUMA/aparc.a2005s+aseg_rank.rankmap.1D
or
Return the entries matching NAME (case insensitive, partial match) from FreeSurfer’s FreeSurferColorLUT.txt Example:
@FS_roi_label -name cerebraYou can use ALL for NAME to get all entries in FreeSurferColorLUT.txt
or
Return the entries matching NAME and their rank per M.1D Unavailable ranks are flagged with the # sign Example:
- @FS_roi_label -name cerebra
- -rankmap SUMA/aparc.a2005s+aseg_rank.rankmap.1D
or
<-labeltable LABELTABLE> <-rankmap M.1D>
Build a label table that can be added to the ranked volume so that AFNI can display labels of parcellated volumes. Use 3drefit -labeltable LABELTABLE DSET to add the table to the rank dataset DSET Example: 3drefit -labeltable LABELTABLE SUMA/aparc.a2005s+aseg_rank
Return the name of an integer labeled area in FreeSurfer’s surface-based annotation.
CMAP is the file output by FSread_annot’s -roi_1D option. It should sit by default in the SUMA/ directory. The script will search a little for a CMAP under the path from where it is launched. However, if the script cannot find a CMAP on its own, you’ll need to specify it with -surf_annot_cmap on the command line.
Return the entries matching NAME (case insensitive, partial match) from the CMAP file Example:
- @FS_roi_label -sname occi
- -surf_annot_cmap lh.aparc.a2005s.annot.1D.cmap