# 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](https://flywheel-io.gitlab.io/scientific-solutions/gears/rtp2-pipeline/index.html).
## Contributing
Please refer to the [CONTRIBUTING.md](CONTRIBUTING.md) file for information on how to
contribute to the gear.
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"description": "# rtp2-pipeline\n\nrtp2-pipeline is a Flywheel Gear that contains a multi-step pipeline designed to run\nMRtrix3, LiFE and SIFT, ET, and obtains tracts and metrics. Necessary ROIs are created\nin the freesurferator gear and the DWI preprocessing is done in rtp2-preproc.\nMRTrix3 + Ensemble Tractography + LiFE generate a connectome which is then run\nthrough a MRtrix3 based tracking system. Then tract profiles of tissue properties\nfor major fiber tracts in the brain are generated. It is possible to create ROI2ROI\ntracts as well. Required inputs are (1) DWI NIfTI image, (2) BVEC file, (3) BVAL file,\n(4) Anatomical NIfTI file, (5) fs.zip with the ROIs in the individual space generated\nby the freesurferator gear, and (6) tractparams.csv, a comma-separated file specifying\nthe details of all the fasciculus to be tracked. If no tractparams is passed, it\nwill provide DTI metrics per ROI. If a qMAP file is passed, it will provide metrics\nat the ROI and/or tract level as well.\n\n## Documentation\n\nThe documentation of the gear can be found\n[here](https://flywheel-io.gitlab.io/scientific-solutions/gears/rtp2-pipeline/index.html).\n\n## Contributing\n\nPlease refer to the [CONTRIBUTING.md](CONTRIBUTING.md) file for information on how to\ncontribute to the gear.\n",
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