Summary of what happened:
the pixel spacing is present but is inside of the (5200,9230).
Command used (and if a helper script was used, a link to the helper script or the command generated): Singularity
heudiconv -d "/database/sub-{subject}_ses-{session}/*/*.dcm" \
-s $subject -ss $session -f /codebase/heuristic.py \
-c dcm2niix -b -o /output --overwrite \
> $LOG_FILE 2> $ERROR_FILE
Version:
heudiconv version 1.3.3
Environment (Docker, Singularity / Apptainer, custom installation):
singularity image , pulled from latest docker image
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Traceback: Traceback (most recent call last): File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 401, in run runtime = self._run_interface(runtime) File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nipype/interfaces/utility/wrappers.py", line 139, in _run_interface out = function_handle(**args) File "<string>", line 35, in embed_dicom_and_nifti_metadata File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/dcmstack/dcmstack.py", line 1163, in parse_and_stack results[key] = stack_group(group, warn_on_except, **stack_args) File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/dcmstack/dcmstack.py", line 1117, in stack_group result.add_dcm(dcm, meta) File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/dcmstack/dcmstack.py", line 520, in add_dcm self._chk_congruent(meta) File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/dcmstack/dcmstack.py", line 479, in _chk_congruent self._chk_close(('PixelSpacing', File "/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/dcmstack/dcmstack.py", line 473, in _chk_close if not np.allclose(meta1[key], meta2[key], atol=5e-5): KeyError: 'PixelSpacing'
`