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Description
I got my hands on Siemens XA61A data (Cima.X), and the localizer causes heudiconv (@yarikoptic FYI) to crash in nibabel code.
Traceback (most recent call last):
File "/home/bpinsard/.virtualenvs/heudiconv_dev/bin/heudiconv", line 8, in <module>
sys.exit(main())
File "/home/bpinsard/.virtualenvs/heudiconv_dev/lib/python3.10/site-packages/heudiconv/cli/run.py", line 30, in main
workflow(**kwargs)
File "/home/bpinsard/.virtualenvs/heudiconv_dev/lib/python3.10/site-packages/heudiconv/main.py", line 410, in workflow
study_sessions = get_study_sessions(
File "/home/bpinsard/.virtualenvs/heudiconv_dev/lib/python3.10/site-packages/heudiconv/parser.py", line 221, in get_study_sessions
seqinfo_dict = group_dicoms_into_seqinfos(
File "/home/bpinsard/.virtualenvs/heudiconv_dev/lib/python3.10/site-packages/heudiconv/dicoms.py", line 342, in group_dicoms_into_seqinfos
mwinfo = validate_dicom(filename, dcmfilter)
File "/home/bpinsard/.virtualenvs/heudiconv_dev/lib/python3.10/site-packages/heudiconv/dicoms.py", line 179, in validate_dicom
del mw.series_signature[sig]
File "/usr/lib/python3.10/functools.py", line 981, in __get__
val = self.func(instance)
File "/home/bpinsard/.virtualenvs/heudiconv_dev/lib/python3.10/site-packages/nibabel/nicom/dicomwrappers.py", line 886, in series_signature
signature['image_shape'] = (self.image_shape, eq)
File "/usr/lib/python3.10/functools.py", line 981, in __get__
val = self.func(instance)
File "/home/bpinsard/.virtualenvs/heudiconv_dev/lib/python3.10/site-packages/nibabel/nicom/dicomwrappers.py", line 775, in image_shape
raise WrapperError("Number of slice indices and positions don't match")
nibabel.nicom.dicomwrappers.WrapperError: Number of slice indices and positions don't match
This is a classic localizer with 3 slices in each plane, but packed into a single enhanced dicoms.
Possibly Siemens is not following some dicoms specs.
dcm2niix v1.0.20240731 (FYI @neurolabusc) is also behaving abnormally, as it stacks the 3 slices in 1 volume, instead of splitting it in separate niftis.
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