Commit 8e1dc6ca authored by Saad Jbabdi's avatar Saad Jbabdi
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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:
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.
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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/etc/xtract/Human or $FSLDIR/etc/xtract/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 '#').
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