7.1.248. @FS_roi_label

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This script is used to get labels associated with FreeSurfer’s parcellation and annotation files.

For volumetric FreeSurfer Parcellations:

Usage: @FS_roi_label <int>

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

Usage: @FS_roi_label <-lab int>

Return the name of an integer labeled area in FreeSurfer’s parcellation Example:

@FS_roi_label -lab 2180

or

Usage: @FS_roi_label <-rank R> <-rankmap M.1D>

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

Usage: @FS_roi_label <-name NAME>

Return the entries matching NAME (case insensitive, partial match) from FreeSurfer’s FreeSurferColorLUT.txt Example:

@FS_roi_label -name cerebra

You can use ALL for NAME to get all entries in FreeSurferColorLUT.txt

or

Usage: @FS_roi_label <-name NAME> <-rankmap M.1D>

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

Usage: @FS_roi_label <-name ALL>
<-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

For Surface-Based FreeSurfer Annotations :

Usage: @FS_roi_label <-surf_annot_cmap CMAP> <-slab int>

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.

Example:
@FS_roi_label -slab 42
-surf_annot_cmap lh.aparc.a2005s.annot.1D.cmap
Usage: @FS_roi_label <-surf_annot_cmap CMAP> <-sname SNAME>

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

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