Attention: Confluence is not suitable for the storage of highly confidential data. Please ensure that any data classified as Highly Protected is stored using a more secure platform.
If you have any questions, please refer to the University's data classification guide or contact ict.askcyber@sydney.edu.au
TractSeg & Tractometry Examples
- Chengtao Liang (Unlicensed)
This page will show examples of Tractseg commands that are currently being tested. Official TractSeg documentation is listed here.
To run TractSeg on Artemis, you will need to load python modules and modules that need to support pytorch. If you are using python/3.6.5 - module load cuda/10.0.130 & openmpi-gcc/3.1.3
For python/3.7.7 - module load magma/2.5.3 & openmpi-gcc/3.1.5
Running TractSeg Tractometry with peaks given from mrtrix3
Continuing from a mrtrix pipeline, you need to extract the peaks of each voxel (sh2peaks).
You will need to run the standard TractSeg pipeline for:
segmentations
Tract Orientation Maps (TOMs)
tractograms
a) Perform tractometry (segment each streamline) using peaks created from mrtrix3 pipeline
#!/bin/bash -v
#PBS -P FFCheng
#PBS -N TractSeg_Tractometry
#PBS -l select=1:ncpus=16:ngpus=1:mem=16GB
#PBS -q=main
#PBS -l walltime=4:00:00
#PBS -q defaultQ
cd $PBS_O_WORKDIR
module load openmpi-gcc/3.1.3
module load cuda/10.0.130
module load python/3.6.5
module load mrtrix3tissue/5.2.7
module load fsl/6.0.3
module load ants/2.3.2
module load mrtrix3/3.0.1
export FSLMETHOD=NONE
tractseg_path=/scratch/FFCheng/DWI_mrtrix_longitudinal/Matched/TractSeg/${sub}/
mkdir ${tractseg_path}
cd ${tractseg_path}
sh2peaks /scratch/FFCheng/DWI_mrtrix_longitudinal/Matched/mrtrix3/DataProcessed/${sub}/tmp/${sub}_wmfod.mif.gz ${tractseg_path}${sub}_peaks.nii.gz
TractSeg -i ${tractseg_path}${sub}_peaks.nii.gz
TractSeg -i ${tractseg_path}${sub}_peaks.nii.gz --output_type endings_segmentation
TractSeg -i ${tractseg_path}${sub}_peaks.nii.gz --output_type TOM
Tracking -i ${tractseg_path}${sub}_peaks.nii.gz --tracking_format tck --nr_fibers 5000
cd ${tractseg_path}tractseg_output
Tractometry -i TOM_trackings/ -o Tractometry.csv -e endings_segmentations/ -s ${tractseg_path}${sub}_peaks.nii.gz --TOM TOM/ --tracking_format tck --peak_length
b) Perform tractometry (segment each streamline) using preprocessed DWI
#mrconvert ${dataproc_path}${sub}_DWI_preprocessed.mif.gz ${tractseg_path}${sub}_DWI_preprocessed.nii.gz -export_grad_fsl ${tractseg_path}${sub}_DWI_preprocessed.bvecs ${tractseg_path}${sub}_DWI_preprocessed.bvals -force
#dwi2tensor ${dataproc_path}${sub}_DWI_preprocessed.mif.gz ${tractseg_path}${sub}_DWI_preprocessed_tensor.mif -force
#tensor2metric ${tractseg_path}${sub}_DWI_preprocessed_tensor.mif -fa ${tractseg_path}${sub}_DWI_preprocessed_FA.nii.gz -force
TractSeg -i ${tractseg_path}${sub}_DWI_preprocessed.nii.gz -o ${tractseg_path} --raw_diffusion_input
TractSeg -i ${tractseg_path}${sub}_peaks.nii.gz --output_type endings_segmentation
TractSeg -i ${tractseg_path}${sub}_peaks.nii.gz --output_type TOM
Tracking -i ${tractseg_path}${sub}_peaks.nii.gz --tracking_format tck --nr_fibers 5000
cd ${tractseg_path}tractseg_output
Tractometry -i TOM_trackings/ -o Tractometry.csv -e endings_segmentations/ -s ${tractseg_path}${sub}_DWI_preprocessed_FA.nii.gz --tracking_format tck
Plotting results
You will need to load the same modules as listed above to plot results.
tractseg_path=/scratch/FFCheng/DWI_mrtrix_longitudinal/Matched/TractSeg/${sub}/
cd /scratch/FFCheng/DWI_mrtrix_longitudinal/Matched/TractSeg/
plot_tractometry_results -i /scratch/FFCheng/DWI_mrtrix_longitudinal/Matched/TractSeg/subjects.txt -o tractometry_result.png --mc