- 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
When running XTRACT with the '-species' option, a predefined list of tracts is automatically extracted. Currently the following tracts are available:
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@@ -119,12 +119,12 @@ When running XTRACT with the '-species' option, a predefined list of tracts is a
Suppose you want to create an automated protocol for a tract called 'mytrack'.
First you need to create a folder called 'mytrack' which you can add e.g. in 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 NIFTI files (with this exact naming) and copy them into mytrack:
**Compulsory**:
- seed.nii.gz : a seed mask
- seed.nii.gz : a seed mask
**Optional**:
- stop.nii.gz : a stop mask if required
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@@ -133,7 +133,7 @@ Then create the following NIFTI files (with this exact naming) and copy them int
- 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
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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@@ -146,27 +146,33 @@ The output of XTRACT is a folder that contrains tracts in separate folders. We p