Add option to skip_dcm2niix and reorganize NIFTI and JSON files

[arnaudbore]

No description provided.

[codecov-commenter]

Codecov Report

Merging #248 (4912381) into master (22a9851) will decrease coverage by 0.39%.
The diff coverage is 21.05%.

@@            Coverage Diff             @@
##           master     #248      +/-   ##
==========================================
- Coverage   78.98%   78.60%   -0.39%     
==========================================
  Files          15       15              
  Lines        1009     1019      +10     
  Branches      214      217       +3     
==========================================
+ Hits          797      801       +4     
- Misses        165      171       +6     
  Partials       47       47              

Flag	Coverage Δ
pytest	78.60% <21.05%> (-0.39%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Changed	Coverage Δ
dcm2bids/dcm2niix_gen.py	48.38% <6.25%> (-4.35%)	⬇️
dcm2bids/cli/dcm2bids.py	55.00% <100.00%> (+0.76%)	⬆️
dcm2bids/dcm2bids_gen.py	80.45% <100.00%> (+0.22%)	⬆️
dcm2bids/utils/utils.py	83.51% <100.00%> (+0.18%)	⬆️

[SamGuay]

Works as it should.

Minor change request:

1. It is possible to run dcm2bids --skip_dcm2niix --force_dcm2niix [...] which is counter-intuitive. The order doesn't matter as --skip_dcm2niix as priority but still feels odd. Also, in the log, it will also add: WARNING | 'force' argument is set to True which can be hard to interpret when we look back at the logs. We could either modify the warning message or add another one.
2. When dcm2bids is run multiple times on the same participant, there is another warning that is technically not true but not harmful: WARNING | Previous dcm2niix directory output found:. If one has NII and json, we can't assume it was produced by dcm2niix.