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xtract_data is the data associated with the XTRACT tool

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, Khrapitchev A, Sallet J, Charquero-Ballester M, Douaud G, 
Jbabdi S*, Mars R*, Sotiropoulos SN* (2020) XTRACT - Standardised protocols for 
automated tractography in the human and macaque brain. 
NeuroImage. DOI: 10.1016/j.neuroimage.2020.116923
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How to create own 'protocol' folder:

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

First you need to create a folder called 'mytrack'.

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


In order to use the protocol masks with XTRACT, you need to defined a seeding strategy in a file called StructureList.

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See e.g. $FSLDIR/data/xtract_data/Human or $FSLDIR/data/xtract_data/Macaque for examples.
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The StructList file is a text file with one entry per tract following this scheme:

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`<tractName> <number>`
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where `<tractName>` matches the protocol folder name (e.g. 'mytrack'), and <number> is the number of streamlines (in thousands) that are seeded from each seed voxel.  This text file can have comments in it (using '#').
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