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xtract_data is the data associated with the XTRACT tool

The HUMAN and MACAQUE tractography protocols were created by:

Rogier Mars, Stamatios Sotiropoulos, Saad Jbabdi, Kathryn Bryant, Shaun Warrington, Marina Charquero-Ballester, Gwenaelle Douaud

The BABY tractography protocols were created by:

Elinor Thompson, Shaun Warrington, Matteo Bastiani, Jessica Dubois, Stamatios Sotiropoulos

The multi-template macaque protocols were created by:

Stephania Assimopoulos, Shaun Warrington, Kathryn Bryant, Rogier Mars, Stamatios Sotiropoulos


The subcortical protocols were created by:

Stephania Assimopoulos, Shaun Warrington, Davide Folloni, Sarah Heilbronner, Stamatios Sotiropoulos

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Citations:

Warrington S., Bryant K., Khrapitchev A., Sallet J., Charquero-Ballester M., Douaud G., Jbabdi S.*, Mars R.*, Sotiropoulos S.N.* (2020) "XTRACT - Standardised protocols for automated tractography in the human and macaque brain". NeuroImage. DOI: 10.1016 j.neuroimage.2020.116923

Warrington S.*, Thompson E.*, Bastiani M., Dubois J., Baxter L., Slater R., Jbabdi S., Mars R.B., and Sotiropoulos S.N. (2022) “Concurrent mapping of brain ontogeny and phylogeny within a common space: Standardized tractography and applications”, Science Advances, vol. 8(42), doi.org/10.1101/2022.03.03.482776

Assimopoulos S., Warrington S., Bryant K.L., Pszczolkowski S., Jbabdi S., Mars R.B., and Sotiropoulos S.N. (2024) "Generalising XTRACT tractography protocols across common macaque brain templates". Brain Struct Funct. DOI: 10.1007/s00429-024-02760-0

Assimopoulos S., Warrington S., Folloni, D., Bryant, K.L., Mohammadi-Nejad A.-R., Tang W., Jbabdi, S., Heilbronner, S.R., Sotiropoulos S.N. (2025) "Cross-species standardised cortico-subcortical tractography". eLife. DOI: 10.7554/eLife.107012

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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.

See e.g. $FSLDIR/data/xtract_data/Human or $FSLDIR/data/xtract_data/Macaque for examples.

The StructList file is a text file with one entry per tract following this scheme:

`<tractName> <number>`

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 '#').