Commit ec7f6a4d authored by Saad Jbabdi's avatar Saad Jbabdi
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more words in README

parent 6106483f
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xtract is a command-line tool for running automated tractography.
### XTRACT is a command-line tool for running automated tractography.
XTRACT can be used to automatically extract a set of carefully dissected tracts in humans and macaques (other
species to come). It can also be used to define one's own tractography protocols where all the user needs to do is to
define a set of masks in standard space (e.g. MNI)
The script was written by Saad Jbabdi & Stamatios Sotiropoulos
(based on the autoPtx tool by Marius de Groot)
(based on the autoPtx tool by Marius de Groot - see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/AutoPtx)
The tractography protocols were created by:
......@@ -14,7 +18,8 @@ Saad Jbabdi, Kathryn Bryant, Shaun Warrington, Marina Charquero-Ballester, Gwena
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Citations:
## Citations:
Warrington S, Bryant K, Charquero-Ballester M, Douaud G, Jbabdi S*, Mars R*, Sotiropoulos SN* (in prep.)
......@@ -27,7 +32,8 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015
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Usage:
## 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]
......@@ -50,19 +56,36 @@ Usage:
-gpu Use GPU version
-native Run tractography in native (diffusion) space
-res <mm> Output resolution (Default=same as in protocol folders unless '-native' used)
```xs
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## Runtime:
XTRACT automatically detects if $SGE_ROOT is set and if so uses FSL_SUB
For optimal performance, use the GPU version!!!!
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Atlases:
- For HUMAN, XTRACT uses the MNI152 standard space in $FSLDIR/etc/standard
- For MACAQUE, XTRACT uses the F99 atlas in Caret - see http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases
We also provide a copy of the F99 atlas in $FSLDIR/etc/xtract_data/standard/F99
This includes a helper script for registering your own diffusion/structural data to the F99 altas
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Adding your own tracts:
## 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.
First you need to create a folder called 'mytrack' which you can add e.g. in the protocols folder.
Then create the following image files (with this exact naming) and copy them into protocols/mytrack:
Then create the following NIFTI files (with this exact naming) and copy them into mytrack:
[Compulsory]:
- seed.nii.gz : a seed mask in MNI152 space
- seed.nii.gz : a seed mask
[Optional]:
- stop.nii.gz : a stop mask if required
......@@ -73,6 +96,6 @@ Then create the following image files (with this exact naming) and copy them int
- 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
All the masks above should be in standard space (e.g. MNI152 or F99) if you want to run the same tracking for a collection of subjects.
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