rtp2-pipeline

rtp2-pipeline is a Flywheel Gear that contains a multi-step pipeline designed to run MRtrix3, LiFE and SIFT, ET, and obtains tracts and metrics. Necessary ROIs are created in the freesurferator gear and the DWI preprocessing is done in rtp2-preproc. MRTrix3 + Ensemble Tractography + LiFE generate a connectome which is then run through a MRtrix3 based tracking system. Then tract profiles of tissue properties for major fiber tracts in the brain are generated. It is possible to create ROI2ROI tracts as well. Required inputs are (1) DWI NIfTI image, (2) BVEC file, (3) BVAL file, (4) Anatomical NIfTI file, (5) fs.zip with the ROIs in the individual space generated by the freesurferator gear, and (6) tractparams.csv, a comma-separated file specifying the details of all the fasciculus to be tracked. If no tractparams is passed, it will provide DTI metrics per ROI. If a qMAP file is passed, it will provide metrics at the ROI and/or tract level as well.

Documentation

The documentation of the gear can be found here.

Contributing

Please refer to the CONTRIBUTING.md file for information on how to contribute to the gear.