Closed asmacdo closed 6 months ago
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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.
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.
FWIW -- pushed 2 little commits to clarify provenance of the docs. Did Dianne state the license?
No but Dianne gave me permission to use her materials upstream.
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
I guess you removed too much -- that is the code/logic in their heuristic. Check which files they care about there.
I'm happy to give back to the community. Attribution is lovely (and makes my bosses happier).
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 :-/
pushed your suggested license commit to see if that kicks off a build
:rocket: PR was released in v1.0.2
:rocket:
:rocket: PR was released in v1.0.2
:rocket:
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:
install
heudiconv
directly, without container in the tutorials