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MRtrix3 / mrtrix3

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density
http://www.mrtrix.org
Mozilla Public License 2.0
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Update HCP (or other) tutorial #1374

Open jdtournier opened 6 years ago

jdtournier commented 6 years ago

As suggested on the forum. Probably best done as a separate page, rather than changing the historical HCP tutorial. But it would be good to have our full 'best practice' pipeline documented from start to finish in one page.

claudebajada commented 6 years ago

Would love to help with this if there is any way that I can contribute.

jdtournier commented 6 years ago

Contributions are always welcome! In this case, the simplest would probably be to add a fresh page in the docs/getting_started/ folder, in reStructuredText format, going through all the steps for a multi-shell pipeline from start to finish. You can work from your own fork, then submit a pull request so we can review it and suggest modifications, etc, and hopefully eventually merge.

Most of the initial processing is common for FBA & tractography analyses, so there shouldn't be a great deal of repetition. That would then serve as a good starting point for most users. It would be good if it was directly applicable as-is to the HCP data, but not essential (we can always add a brief section to describe how to get the HCP data into a format where the pipeline can be applied as-is).

Thanks!

claudebajada commented 6 years ago

Thanks, I will probably start next Monday as it is a holiday / long weekend around here from tomorrow

eds-slim commented 7 months ago

Is there any update on this? I also think that having current best practices documented would be very helpful. Thanks!