Enhanced dicom fixes

[akhanf]

This tries to address the specific issues in #44, related to the CFMM 3T software upgrade.

1. fixes parsing to accept more generic StudyID tags from the filename
2. updates the cfmm_base heuristic to allow 'NONE' to mean the same thing as 'ND' when checking whether there is any distortion correction (e.g. DIS2D, DIS3D) applied to the image.
3. updates to latest heudiconv and dcm2niix, as they include fixes to get enhanced dicom on Siemens data to work.

The issue is that the Bruker enhanced dicoms still require our custom fork (https://github.com/AlanKuurstra/heudiconv, branch=unstacked_dcm). @AlanKuurstra, what was the reason we opted to not make a PR into heudiconv for those changes? That would be the ideal situation, otherwise we could perhaps just update that branch with latest heudiconv changes and continue as is (perhaps that is what we do in the short-term anyhow)..

[AlanKuurstra]

Two issues needed to be addressed when we forked heudiconv, one regarding time zones and the other metadata.

The time zone changes have now been merged upstream.
nipy/heudiconv#780

The additional problem of filling the metadata sidecar file with 4d and 5d dicom metadata is not resolved upstream afaik. The problem needs to be addressed in one of heudiconv’s dependencies, dcmstack:
moloney/dcmstack#84
If none of our users are using the additional metadata, I would suggest using the official heudiconv repo and employing the minmeta option which will avoid the metadata bug until the changes in dcmstack have been merged.

Honestly, we may want to use minmeta by default even after upstream supports n-d enhanced dicoms. Heudiconv converts dicom to nifti using dcm2niix, but if minmeta is not used it will convert the dicom to nifti a second time with dcmstack only for the purpose of concatenating dicom metadata for the bids sidecar file, which is inefficient especially for some of our larger datasets.

If users need more metadata than is provided with the minmeta option, we can always require them to extract it themselves using their heuristics file and defining a custom_callable function as done here

[akhanf]

I posted this in the issue, but repeating here for context

The use of --minmeta wasn't making a difference for me (ie it was still choking on the Bruker dicoms), and applying the commit you had (nipy/heudiconv@def8691) to the latest heudiconv doesn't fix things either, not sure if it is the same issue or a new one though..

alik@AFI-CBS-H-1:/local/scratch$ singularity run -e ./tar2bids_enhdicom.sif -h cfmm_bruker.py -O "--minmeta" -o test_enhdicom_bruker_updated_minmeta -P '{subject}' Everling_Marmoset_20230718_Betty_20230718_01.484D54A4.tar
	Overriding heuristic file as: cfmm_bruker.py
	Using heudiconv options: --minmeta
	Overriding output dir as: test_enhdicom_bruker_updated_minmeta
  Using custom PatientName search: {subject}
  PI=Everling Study=Marmoset Date=20230718 PatientName=Betty
session not found in {subject}
Everling_Marmoset_20230718_Betty_20230718_01.484D54A4.tar -> sub-Betty
  Running: heudiconv ... 
heudiconv --minmeta --overwrite -b -d /local/scratch/Everling_Marmoset_20230718_\{subject\}_20230718_01.484D54A4.tar -o /local/scratch/test_enhdicom_bruker_updated_minmeta -f /opt/tar2bids/heuristics/cfmm_bruker.py -s Betty  | tee /local/scratch/test_enhdicom_bruker_updated_minmeta/code/tar2bids_2024-11-20_11h13m_32370/logs/heudiconv.Betty
INFO: Running heudiconv version 1.3.2+enhdicom.0 latest 1.3.2
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': 'Betty', 'outdir': '/local/scratch/test_enhdicom_bruker_updated_minmeta/', 'session': None}
INFO: Processing 19 dicoms
INFO: Analyzing 19 dicoms
Traceback (most recent call last):
  File "/usr/local/bin/heudiconv", line 33, in <module>
    sys.exit(load_entry_point('heudiconv==1.3.2+enhdicom.0', 'console_scripts', 'heudiconv')())
  File "/usr/local/lib/python3.9/dist-packages/heudiconv/cli/run.py", line 30, in main
    workflow(**kwargs)
  File "/usr/local/lib/python3.9/dist-packages/heudiconv/main.py", line 479, in workflow
    prep_conversion(
  File "/usr/local/lib/python3.9/dist-packages/heudiconv/convert.py", line 217, in prep_conversion
    seqinfo = group_dicoms_into_seqinfos(
  File "/usr/local/lib/python3.9/dist-packages/heudiconv/dicoms.py", line 338, in group_dicoms_into_seqinfos
    mwinfo = validate_dicom(filename, dcmfilter)
  File "/usr/local/lib/python3.9/dist-packages/heudiconv/dicoms.py", line 175, in validate_dicom
    del mw.series_signature[sig]
  File "/usr/lib/python3.9/functools.py", line 969, in __get__
    val = self.func(instance)
  File "/usr/local/lib/python3.9/dist-packages/nibabel/nicom/dicomwrappers.py", line 886, in series_signature
    signature['image_shape'] = (self.image_shape, eq)
  File "/usr/lib/python3.9/functools.py", line 969, in __get__
    val = self.func(instance)
  File "/usr/local/lib/python3.9/dist-packages/nibabel/nicom/dicomwrappers.py", line 770, in image_shape
    raise WrapperError('Non-singular index precedes the slice index')
nibabel.nicom.dicomwrappers.WrapperError: Non-singular index precedes the slice index

I think I will just merge this PR to get the 3T functional again, then can make a new issue for the above