Commit 1a9dfa38 authored by Shaun Warrington's avatar Shaun Warrington
Browse files

changes to readme

parent 67fce2d3
......@@ -70,8 +70,47 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015
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## Running XTRACT:
XTRACT automatically detects if $SGE_ROOT is set and if so uses FSL_SUB.
For optimal performance, use the GPU version!!!!
XTRACT automatically detects if $SGE_ROOT is set and if so uses FSL_SUB. For optimal performance, use the GPU version!!!!
Outputs of XTRACT
Under <outputDir>:
- "commands.txt" - XTRACT processing commands
- "logs" - directory containing the probtrackx log files
- "tracts" - directory continaing tractography results
-- "<tractName>" - directory per tract, each continaing:
-- "waytotal" - txt file continaing the number of valid streamlines
-- "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
-- "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:
--- "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
-- If the "-native" option is being used:
--- "masks" - directory
--- "<tractName>" - directory per tract continaing the native space protocol masks
The primary output is the "densityNorm.nii.gz" file.
Pre-processing
Prior to running XTRACT, you must complete the FDT processing pipeline:
Brain extraction using BET
Susceptibility distortion correction using topup (only if spin-echo fieldmaps have been acquired - if you don't have these, skip to step 3)
Eddy current distortion and motion correction using eddy
Fit the crossing fibre model using bedpostx
Registration to standard space (MNI152), see the FDT pipeline
Your data should now be ready to run XTRACT!
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