AnchorBar

AnchorBar (aka "Analyzer") is a Python program developed to maintain and compute set operations on FreeSurfer annotation files. It's kind of like SPM's MarsBar plugin, but for FreeSurfer.

Requirements

AnchorBar has a few dependencies that must be met:

1. argparse
2. sqlite3
3. hashlib
4. nibabel
5. random
6. numpy

Attempting to run the scripts will fail and report missing libraries. They can be installed using pip:

pip install nibabel

The utility is (currently) comprised of 3 scripts. Syntax help for each of these scripts can be obtained using the -h switch:

$ AnchorBar_tools.py -h
usage: AnchorBar_tools.py [-h] [--list] [--labels annot_id] [--db DB] [--rename annot_id new_shortname]
                         [--relabel annot_id label_id new_label_name] [--abbrev annot_id label_id abbrev_label_name]

Querying Available Annotations

AnchorBar_tools.py provides tools to list, rename and relabel annotations. Each annotation has a unique ID and descriptors indicating the hemisphere, a shortname used for naming labels generated from set operations, and a path indicating the file path of the source .annot file. The default set of annotations stored in annot.db includes the 10 pairs of lhrh annotations from fsaverage/label:

AnchorBar_tools.py --db annot.db --list