Multi-stack ID for DICOM Files. Running DICOM to Nifti conversion through Singularity container

[s-madhavan]

Hi everyone,

I am running Dicom to Nifti conversion using heudiconv and keep getting this error. Can't seem to find anything for anyone else that has had the same issue, and how they resolved it.

Issue raised on github heudiconv: nipy/heudiconv#455
Scanner is Phillips scanner.

Starting BIDS conversion for subject YA-0690344E_20231114-20231114 1
WARNING: Environment variable LD_PRELOAD already has value [], will not forward new value [/apps/xalt/xalt/lib64/libxalt_init.so] from parent process environment
INFO: Running heudiconv version 1.1.0 latest 1.1.0
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': 'YA-0690344E_20231114-20231114', 'outdir': '/fs/ess/PAS2302/Subbi/TURBO/TERBO/Nifti/', 'session': '1'}
INFO: Processing 10 dicoms
WARNING: 'YA-0690344E_20231114-20231114' label contained non-alphanumeric character(s), it was cleaned to be 'YA0690344E2023111420231114'
INFO: Analyzing 10 dicoms
Traceback (most recent call last):
  File "/opt/miniconda-py39_4.12.0/bin/heudiconv", line 8, in <module>
    sys.exit(main())
  File "/src/heudiconv/heudiconv/cli/run.py", line 30, in main
    workflow(**kwargs)
  File "/src/heudiconv/heudiconv/main.py", line 479, in workflow
    prep_conversion(
  File "/src/heudiconv/heudiconv/convert.py", line 217, in prep_conversion
    seqinfo = group_dicoms_into_seqinfos(
  File "/src/heudiconv/heudiconv/dicoms.py", line 324, in group_dicoms_into_seqinfos
    mwinfo = validate_dicom(filename, dcmfilter)
  File "/src/heudiconv/heudiconv/dicoms.py", line 161, in validate_dicom
    del mw.series_signature[sig]
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/onetime.py", line 156, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py", line 628, in series_signature
    signature['image_shape'] = (self.image_shape, eq)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/onetime.py", line 156, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py", line 539, in image_shape
    raise WrapperError(
**nibabel.nicom.dicomwrappers.WrapperError: File contains more than one StackID. Cannot handle multi-stack files
Finished subject YA-0690344E_20231114-20231114 1**

Thank you.

--Subbi M.

[effigies]

We will need someone familiar with these DICOMs to understand what the result should be and provide test data before we can fix them. @moloney is this something you've seen before?