xtract is a command-line tool for running automated tractography.

The script was written by Saad Jbabdi & Stamatios Sotiropoulos (based on the autoPtx tool by Marius de Groot)

The tractography protocols were created by:

Rogier Mars & Stamatios Sotiropoulos

with help from: Saad Jbabdi, Kathryn Bryant, Shaun Warrington, Marina Charquero-Ballester, Gwenaelle Douaud


Citations:

Warrington S, Bryant K, Charquero-Ballester M, Douaud G, Jbabdi S*, Mars R*, Sotiropoulos SN* (in prep.) Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain.

de Groot M; Vernooij MW. Klein S, Ikram MA, Vos FM, Smith SM, Niessen WJ, Andersson JLR (2013) Improving alignment in Tract-based spatial statistics: Evaluation and optimization of image registration. NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015


Usage:


Adding your own tracts:

Suppose you want to create an automated protocol for a tract called 'mytrack'.

First you need to create a folder called 'protocols/mytrack' within the protocols folder.

Then create the following image files (with this exact naming) and copy them into protocols/mytrack:

[Compulsory]: - seed.nii.gz : a seed mask in MNI152 space

[Optional]: - stop.nii.gz : a stop mask if required - exclude.nii.gz : an exclusion mask if required - ONE of the following:

- invert (empty file to indicate that a seed->target and target->seed run will be added and combined)

 

UserGuide (last edited 14:55:47 03-07-2019 by SaadJbabdi)