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

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

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The tractography protocols were created by:

Rogier Mars & Stamatios Sotiropoulos

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


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Citations:

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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

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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

    Optional arguments:

       -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)

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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