quality analysis after pre-processing

[Remi-Gau]

This will use spmup to create a quality control pipeline after pre-processing.

This won't replace fMRIprep and is not meant to but some of us can't unfortunately fMRIprep on their data. 😢

So far this reuses a lot of the BIDS pipeline that exists already as part of spmup.

• check that spmup runs on octave

[Remi-Gau]

should implement several aspects of #67

[codecov]

Codecov Report

Merging #98 into dev will decrease coverage by 1.35%.
The diff coverage is 40.41%.

@@            Coverage Diff             @@
##              dev      #98      +/-   ##
==========================================
- Coverage   46.52%   45.17%   -1.36%     
==========================================
  Files          59       66       +7     
  Lines        1324     1388      +64     
==========================================
+ Hits          616      627      +11     
- Misses        708      761      +53     

Impacted Files	Coverage Δ
src/QA/anatomicalQA.m	0.00% <0.00%> (ø)
src/QA/functionalQA.m	0.00% <0.00%> (ø)
src/concatBetaImgTmaps.m	0.00% <0.00%> (ø)
src/mancoreg/mancoregCallbacks.m	0.00% <0.00%> (ø)
src/spmBatching/bidsResliceTpmToFunc.m	0.00% <0.00%> (ø)
src/spmBatching/setBatchFactorialDesign.m	0.00% <0.00%> (ø)
src/spmBatching/setBatchMeanAnatAndMask.m	0.00% <0.00%> (ø)
src/spmBatching/setBatchReslice.m	0.00% <0.00%> (ø)
src/spmBatching/setBatchSubjectLevelGLMSpec.m	0.00% <0.00%> (ø)
src/spmBatching/setBatchRealign.m	67.85% <80.00%> (ø)
... and 23 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update b6938fc...2838c42. Read the comment docs.

[Remi-Gau]

• make output of QA more BIDS derivative compatible
  • confounds file with dictionary

might require some fix in spmup
CPernet/spmup#15

[Remi-Gau]

• separate anat and func QA pipeline
• add tests