Update nextflow pipeline to add processing

courtois-neuromod / anat-processing

Pipeline to process anatomical data, including microstructure metrics from DWI and MT data

MIT License

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Closed jcohenadad closed 2 years ago

jcohenadad commented 3 years ago

The initial NF pipeline started with the MTsat pipeline copied from this repos.

We need to add the following processing:

DWI
- Currently there is a tractoflow pipeline, that outputs DTI maps and performs tractography
MTR
- registration to T1w MPRAGE (so we can use the masks)
T1 mapping from the MP2RAGE data
Spinal Cord: process MTR/sat, DWI,
Extraction of metrics: will be done in notebook, see https://github.com/courtois-neuromod/anat-processing/issues/3

agahkarakuzu commented 2 years ago

SCT is no longer using Nextflow, closing the issue.