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:
xtract -bpx <bedpostX_dir> -out <outputDir> -str <structuresFile> -p <protocolsFolder> [options] xtract -bpx <bedpostX_dir> -out <outputDir> -species HUMAN [options] xtract -bpx <bedpostX_dir> -out <outputDir> -species MACAQUE [options] Compulsory arguments:
-bpx <folder> Path to bedpostx folder -out <folder> Path to output folder And EITHER:
-str <file> Structures file (format: <tractName> [samples=1], 1 means 1000, '#' to skip lines) -p <folder> Protocols folder (all masks in same standard space) Or:
-species <SPECIES> One of HUMAN or MACAQUE
-stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard}) -gpu Use GPU version -native Run tractography in native (diffusion) space -res <mm> Output resolution (Default=same as in protocol folders unless '-native' used)
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:
- - target.nii.gz : a single target mask - target1.nii.gz, target2.nii.gz, etc. : a number of targets, in which case streamlines will be kept if they cross ALL of them
- invert (empty file to indicate that a seed->target and target->seed run will be added and combined)
- if such an option is required a single "target.nii.gz" file is also expected