connectomemapper3
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ENH: Implementation of FSL topup for DWI preprocessing
Following the issue #18 to integrate FSL topup correction (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup) in the diffusion pipeline
Tasks I see so far:
-
[ ] Implementation of a new Nipype interface specific to FSL topup in
cmtklib/interfaces/fsl.py
OR an existing interface might be already implemented inside Nipype (not checked yet) -
[ ] Update of the interface to FSL eddy in
cmtklib/interfaces/fsl.py
which should now take as possible input the output of FSL topup. -
[ ] Update of the main subworkflow dedicated to the preprocessing of DWI data (in
cmp/stages/preprocessing/preprocessing.py
). Workflow should be updated or inputs/outputs of interfaces should be rearranged appropriately with the new OR modified interface in the functioncreate_workflow
of the classPreprocessingStage
. Option for enabling/disabling should be added as a Boolean class attribute/trait to the classPreprocessingConfig
.
Note: More parameters related to FSL topup itself must also be added there.
-
[ ] If necessary, update the main diffusion workflow (in
cmp/pipelines/diffusion/diffusion.py
). This might involve updating outputs to be sinked to the main CMP3 outputs (<derivatives>/cmp/dwi
). -
[ ] New attributes/traits can then be easily integrated and tuned in the graphical user interface by an appropriate update of the corresponding graphical component, implemented in
cmp/bidsappmanager/stages/preprocessing/preprocessing.py