-- "<tractName>" - directory per tract, each continaing:
- "<tractName>" - directory per tract, each continaing:
-- "waytotal" - txt file continaing the number of valid streamlines
- "waytotal" - txt file continaing the number of valid streamlines
-- "density.nii.gz" - nifti file containing the fibre probability distribution
- "density.nii.gz" - nifti file containing the fibre probability distribution
-- "density_lenths.nii.gz" - nifti file containing the fibre lengths, i.e. each voxel is the average streamline length - this is the "-ompl" probtrackx option
- "density_lenths.nii.gz" - nifti file containing the fibre lengths, i.e. each voxel is the average streamline length - this is the "-ompl" probtrackx option
-- "densityNorm.nii.gz" - nifti file continaing the waytotal normalised fibre probability distribution (the "density.nii.gz" divided by the total number of valid streamlines)
- "densityNorm.nii.gz" - nifti file continaing the waytotal normalised fibre probability distribution (the "density.nii.gz" divided by the total number of valid streamlines)
-- If the protocol calls for reverse-seeding:
- If the protocol calls for reverse-seeding:
--- "tractsInv" - directory continaing the above for the seed-target reversed run
- "tractsInv" - directory continaing the above for the seed-target reversed run
--- "sum_waytotal" and "sum_density.nii.gz" - the summed waytotal and fibre probability distribution
- "sum_waytotal" and "sum_density.nii.gz" - the summed waytotal and fibre probability distribution
-- If the "-native" option is being used:
- If the "-native" option is being used:
--- "masks" - directory
- "masks" - directory
--- "<tractName>" - directory per tract continaing the native space protocol masks
- "<tractName>" - directory per tract continaing the native space protocol masks
The primary output is the "densityNorm.nii.gz" file.
The primary output is the "densityNorm.nii.gz" file.
Pre-processing
**Pre-processing**
Prior to running XTRACT, you must complete the FDT processing pipeline:
Prior to running XTRACT, you must complete the FDT processing pipeline:
Brain extraction using BET
1. Brain extraction using BET
2. Susceptibility distortion correction using topup (only if spin-echo fieldmaps have been acquired - if you don't have these, skip to step 3)
Susceptibility distortion correction using topup (only if spin-echo fieldmaps have been acquired - if you don't have these, skip to step 3)
3. Eddy current distortion and motion correction using eddy
4. Fit the crossing fibre model using bedpostx
Eddy current distortion and motion correction using eddy
5. Registration to standard space (MNI152), see the FDT pipeline
6. Your data should now be ready to run XTRACT!
Fit the crossing fibre model using bedpostx
Registration to standard space (MNI152), see the FDT pipeline