Add dianne tutorials

[asmacdo]

This PR adds some tutorials from Dianne Patterson at University of Arizona: https://neuroimaging-core-docs.readthedocs.io/en/latest/index.html (with permission, thanks Dianne!)

I've moved some things around so the left bar didn't get so cluttered.

Remaining TODOs:

• Fix links to outside docs
• Example Dataset
  • Convert example data to datalad dataset
  • Remove unused files
  • push to http://datasets.datalad.org/
• Add Podman option to install
• Use heudiconv directly, without container in the tutorials
• Add Docker/Podman example commands to CLI reference
• convert hdc_run.sh to docs

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (81f0d2f) 81.97% compared to head (e0f9ce2) 81.97%.
Report is 4 commits behind head on master.

Additional details and impacted files

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##           master     #734   +/-   ##
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  Coverage   81.97%   81.97%           
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  Files          41       41           
  Lines        4149     4149           
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  Hits         3401     3401           
  Misses        748      748           

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[TheChymera]

Looks good to me, other than failing lint/spell.

One thing though, I don't think “Heuristic File Reference” makes it any clearer.
If anything it's more confusing....

As per the discussion on Monday, you did mention heuristic is a bit vague.
I would say — and it might be some professional jargon I picked up — that “heuristic” is a pretty clear concept in parsing/reformatting things.
If you feel clarification is needed, perhaps “Heuristic Specification File” would be clearer, i.e. the file which specifies the heuristic.

[yarikoptic]

I would not abuse "specification" word here: if used explicitly it usually refers to some formalized semantic description (e.g. recipe as amounts of each incredient, not really the cooking instructions per se). Heuristic ATM is Python code to provide desired organization (directories) and names to the files given DICOMs metadata.

[yarikoptic]

FWIW -- pushed 2 little commits to clarify provenance of the docs. Did Dianne state the license?

[asmacdo]

No but Dianne gave me permission to use her materials upstream.

[asmacdo]

Goal: make the example dataset minimal (delete extra files)

I tried deleting all sequences except DTI_30_DIRs_AP_15, but it failed

    Traceback (most recent call last):
      File "/home/austin/miniconda3/bin/heudiconv", line 8, in <module>
        sys.exit(main())
                 ^^^^^^
      File "/home/austin/miniconda3/lib/python3.11/site-packages/heudiconv/cli/run.py", line 30, in main
        workflow(**kwargs)
      File "/home/austin/miniconda3/lib/python3.11/site-packages/heudiconv/main.py", line 479, in workflow
        prep_conversion(
      File "/home/austin/miniconda3/lib/python3.11/site-packages/heudiconv/convert.py", line 237, in prep_conversion
        info = heuristic.infotodict(seqinfo_list)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/austin/datasets/sub-219_dicom/MRIS/Nifti/code/heuristic1.py", line 106, in infotodict
        raise ValueError('\n'.join(msg))
    ValueError: WARNING: Missing correct number of T1w runs
    WARNING: Missing correct number of RPE runs
    WARNING: Missing correct number of magnitude runs
    WARNING: Missing correct number of phasediff runs
    WARNING: Missing correct number of resting_state runs
    WARNING: Missing correct number of resting_state_post runs

[yarikoptic]

I guess you removed too much -- that is the code/logic in their heuristic. Check which files they care about there.

[asmacdo]

Currently the tutorial still makes some assumptions about user-knowledge of MRIs BIDs, which might be just fine for this project-- I just need someone more familiar to review.

[asmacdo]

@yarikoptic This section needs review from someone who is more familiar with bids/reproin/mri

[dkp]

I'm happy to give back to the community. Attribution is lovely (and makes my bosses happier).

[yarikoptic]

don't know yet why RTD does not report back on builds, although it does them for PRs e.g. https://readthedocs.org/projects/heudiconv/builds/23301131/ . I have checked oauth permissions on personal and nipy org levels -- all seems good. I found that there were 2 instead of one webhooks for github , removed one and resynced another. Let's see if may be it would emerge back

edit: actually for this PR 734 the last one from 2 weeks ago. The most recent one was for #735 from a day ago and there it reported fine. So something must be special about this PR :-/

[yarikoptic]

all good, again independent of the goal of the PR

[asmacdo]

pushed your suggested license commit to see if that kicks off a build

[yarikoptic]

Says "Here" like there would be an image like those https://github.com/ReproNim/reproin/blob/master/docs/walkthrough-1.md#new-program
anything missing?

[github-actions]

🚀 PR was released in v1.0.2 🚀

[github-actions]

🚀 PR was released in v1.0.2 🚀