TRACULA: TRActs Contrained by UnderLying Anatomy

TRACULA is tool for automatic reconstruction of a set of major white-matter pathways from diffusion-weighted images. It uses global probabilistic tractography with anatomical priors. Prior distributions on the neighboring anatomical structures of each pathway are derived from an atlas and combined with the FreeSurfer cortical parcellation and subcortical segmentation of the subject that is being analyzed to constrain the tractography solutions. This obviates the need for user interaction, e.g., to draw ROIs manually or to set thresholds on path angle and length, and thus automates the application of tractography to large datasets.

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Documentation

The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user's preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.

Tutorials

For step by step instruction on how to set up and run TRACULA, please refer to the relevant tutorials from the FreeSurfer training workshops:

Reference

Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy. Yendiki A, Panneck P, Srinivasan P, Stevens A, Zöllei L, Augustinack J, Wang R, Salat D, Ehrlich S, Behrens T, Jbabdi S, Gollub R and Fischl B (2011). Front. Neuroinform. 5:23. doi: 10.3389/fninf.2011.00023