TheLabbingProject / django_mri

A reusable Django app to manage MRI data.
https://django-mri.readthedocs.io/en/latest/
Apache License 2.0
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Interface to TheBase-appropriate dMRIPrep #153

Closed GalKepler closed 2 years ago

GalKepler commented 2 years ago

I've created an interface to dmriprep pipeline that is suited to handle TheBase complex fieldmap scheme. I've also made sure that the environment, although not set by a docker container (yet) is equipped to handle the pipeline.

The things we need to do in order to run it over our dataset are:

  1. Create a runner.
  2. Make sure the interface is all set (I'm not sure I remembered everything that needs to be done).
  3. ~Recreate "REV" encoded fieldmaps as a single-volume image under "fmap" BIDS datatype (an issue about this has already been opened, #152).~

Anyway, this fixes #151

codecov[bot] commented 2 years ago

Codecov Report

Merging #153 (d3eada0) into master (ba34f2e) will decrease coverage by 0.80%. The diff coverage is 12.60%.

@@            Coverage Diff             @@
##           master     #153      +/-   ##
==========================================
- Coverage   43.78%   42.97%   -0.81%     
==========================================
  Files         238      241       +3     
  Lines        4840     4933      +93     
  Branches      602      619      +17     
==========================================
+ Hits         2119     2120       +1     
- Misses       2698     2790      +92     
  Partials       23       23              
Impacted Files Coverage Δ
...o_mri/analysis/interfaces/dmriprep_bak/dmriprep.py 0.00% <0.00%> (ø)
...o_mri/analysis/interfaces/dmriprep_bak/messages.py 0.00% <0.00%> (ø)
...ango_mri/analysis/interfaces/dmriprep_bak/utils.py 0.00% <0.00%> (ø)
django_mri/analysis/mri_interfaces.py 0.00% <0.00%> (ø)
...jango_mri/analysis/interfaces/dmriprep/dmriprep.py 31.03% <34.78%> (-3.12%) :arrow_down:
django_mri/analysis/analysis_definitions.py 96.72% <100.00%> (ø)
...jango_mri/analysis/interfaces/dmriprep/messages.py 100.00% <100.00%> (+100.00%) :arrow_up:
django_mri/analysis/interfaces/dmriprep/utils.py 100.00% <100.00%> (ø)
...o_mri/analysis/specifications/dmriprep/dmriprep.py 100.00% <100.00%> (ø)

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