Track the Anterior Limb of the Internal Capsule

This application produces a streamline-based model of the anterior limb of the internal capsule. It further divides its output into a superior (canonical) and inferior (non-canonical) components.

There are three primary steps in this methodlology:

1. Identification of the anterior limb white matter volume. This is acheived by identifying anatomical landmarks withing the subject’s brain (using the freesurfer Desikan-Killiany parcellation). This is performed by the app-track-between-multiple-regions/produce_aLIC_ROIs.py script.
2. Performance of targeted, ensemble tractography. This algorithm iterates across parameter settings to create a broadly sampled tractogram. The current implementation is essentialy a copy of an existing app/resource (currently entitled “RACE-Track”) developed and maintaned by Brent McPherson. This is performed by the app-track-between-multiple-regions/mrtrix3_tracking.sh script.
3. Segmentation of the resultant tractogram, to produce a curated model of the anterior limb of the internal capsule. Although MRtrix3 and RACE-Track produce quality tractography models, further curation is needed to ensure adherence to constraints of biological plausibility and contemporary understanding of the structure’s morphology. This is acheived via a White Matter Query Language (WMQL)-like method that has been used in previous publications and has been comprehensively described in the White Matter Segentation Education (WIMSE) resource (website here). It is performed by the segViaDocker/seg_aLIC_connections.py script.