heudiconv v1.3.4 gives error number of slice indices and positions don't match

[akelkar26]

Hi,

I am running heudiconv v1.3.4 to convert dicoms to nifti files (for later bids conversion and .tsv file generation) on Siemens XA60 enhanced dicoms.

Here is my command:
docker run --rm -it \ -v /Users/neurouser1/Documents/CLWM_Scans:/base \ nipy/heudiconv:1.3.4 \ -d /base/raw_data/sub-{subject}/ses-{session}/scans/\*/resources/DICOM/files/\*.dcm \ -o /base/niftifiles/ \ -f convertall \ -s DYMI \ -ss test \ -c none \

However, I get this error:
WARNING: Could not check for version updates: Connection to server could not be made INFO: Running heudiconv version 1.3.4 latest Unknown INFO: Need to process 1 study sessions INFO: PROCESSING STARTS: {'subject': 'DYMI', 'outdir': '/base/niftifiles/', 'session': 'test'} INFO: Processing 968 dicoms INFO: Analyzing 968 dicoms Traceback (most recent call last): File "/opt/miniconda-py39_4.12.0/bin/heudiconv", line 7, 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 480, in workflow prep_conversion( File "/src/heudiconv/heudiconv/convert.py", line 215, in prep_conversion seqinfo = group_dicoms_into_seqinfos( File "/src/heudiconv/heudiconv/dicoms.py", line 338, in group_dicoms_into_seqinfos mwinfo = validate_dicom(filename, dcmfilter) File "/src/heudiconv/heudiconv/dicoms.py", line 203, in validate_dicom del mw.series_signature[sig] File "/opt/miniconda-py39_4.12.0/lib/python3.9/functools.py", line 993, in __get__ val = self.func(instance) File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py", line 886, in series_signature signature['image_shape'] = (self.image_shape, eq) File "/opt/miniconda-py39_4.12.0/lib/python3.9/functools.py", line 993, in __get__ val = self.func(instance) File "/opt/miniconda-py39_4.12.0/lib/python3.9/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

I saw a patch was made in September so I am using the latest available version. However, the issue still exists for our data.

Could you please advise?

Thank you
Best,
Apoorva

[yarikoptic]

what version of nibabel? e.g. (seems to be current)

❯ python -c 'import nibabel as nib; print(nib.__version__)'
5.3.2

[akelkar26]

Hello,

Would you have an insight on how to fix this issue?
Thank you
Best,
Apoorva

[yarikoptic]

@akelkar26 please reply first to the question I asked

[peaceisbetter]

@akelkar26 please reply first to the question I asked

I am getting the same error form the original post and I am using nibabel version 5.3.2 with heudiconv version 1.3.4.

Traceback (most recent call last):
  File "/opt/miniconda-py39_4.12.0/bin/heudiconv", line 7, 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 480, in workflow
    prep_conversion(
  File "/src/heudiconv/heudiconv/convert.py", line 215, in prep_conversion
    seqinfo = group_dicoms_into_seqinfos(
  File "/src/heudiconv/heudiconv/dicoms.py", line 338, in group_dicoms_into_seqinfos
    mwinfo = validate_dicom(filename, dcmfilter)
  File "/src/heudiconv/heudiconv/dicoms.py", line 203, in validate_dicom
    del mw.series_signature[sig]
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/functools.py", line 993, in __get__
    val = self.func(instance)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py", lin series_signature
    signature['image_shape'] = (self.image_shape, eq)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/functools.py", line 993, in __get__
    val = self.func(instance)
  File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py", lin 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
> /opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nibabel/nicom/dicomwrappers.py(775)image_
-> raise WrapperError("Number of slice indices and positions don't match")

It looks like the error may be that I have localizers in my dicoms files and the nibabel version 5.3.2 may have a more strict check for 3D images than previous nibabel versions (this is my naive interpretation).