Fix missing file paths in 02_proc-dwi and 03_SC

MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below

http://micapipe.readthedocs.io

GNU General Public License v3.0

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Fix missing file paths in 02_proc-dwi and 03_SC #67

Closed araikes closed 1 year ago

araikes commented 1 year ago

There were a number of file paths that were either missing or changed in 0.1.5 leading to downstream processing issues (#64). This updates file paths from *.mif to *.nii.gz where necessary, adds an output path for mrdegibbs, and capitalizes T1w in the call to json_nativepro_T1w

rcruces commented 1 year ago

Hello, thank you for your collaboration. We've been working on a lot of improvements of the pipeline in the past 3 months. And we just released a new version v0.2.0, we really encourage to use it, because it has been optimized and fully revised before the deploy.
I will close this pull request to master (now is v0.2.0). You could re open the pull request to the other branch v0.1.5 (https://github.com/MICA-MNI/micapipe/tree/micapipe_v0.1.5), so I can revise the changes there.

Thank you so much