ERROR: Embedding failed

[ibrwr]

Summary

Hi all,

My conversion seem to go well, i get nifti and populated json files. But very often I get the error "ERROR: Embedding failed: Exception raised while executing Node embedder."

Do I understand correctly that this is dcmstack crashing on some values it found in the dicom file and therefore the only result is that some extra information is missing in the json file but to solve it, it would need to be fixed in dcmstack?

Thanks for help!

Iman

Platform details:

Choose one:

• Local environment: version 10.0 on python 3.6.8 on Rad Hat Linux

• [ x] Container 9.0.0

• Heudiconv version: dependent on environment, see above

211210-13:05:33,955 nipype.workflow INFO:
[Node] Setting-up "embedder" in "/tmp/embedmetapm5_9hl7/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetapm5_9hl7/embedder".
211210-13:05:33,960 nipype.workflow INFO:
[Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
211210-13:05:33,971 nipype.workflow INFO:
[Node] Finished "embedder", elapsed time 0.010596s.
INFO: [Node] Finished "embedder", elapsed time 0.010596s.
211210-13:05:33,971 nipype.workflow WARNING:
Storing result file without outputs
WARNING: Storing result file without outputs
211210-13:05:33,972 nipype.workflow WARNING:
[Node] Error on "embedder" (/tmp/embedmetapm5_9hl7/embedder)
WARNING: [Node] Error on "embedder" (/tmp/embedmetapm5_9hl7/embedder)
ERROR: Embedding failed: Exception raised while executing Node embedder.

Traceback (most recent call last):
File "/<shortened_path>/heudiconv_venv_10.0/lib64/python3.6/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/<shortened_path>/heudiconv_venv_10.0/lib64/python3.6/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
out = function_handle(**args)
File "", line 28, in embed_dicom_and_nifti_metadata
File "/<shortened_path>/heudiconv_venv_10.0/lib64/python3.6/site-packages/dcmstack/dcmstack.py", line 1223, in parse_and_stack
warn_on_except)
File "/<shortened_path>/heudiconv_venv_10.0/lib64/python3.6/site-packages/dcmstack/dcmstack.py", line 1126, in parse_and_group
meta = extractor(dcm)
File "/<shortened_path>/heudiconv_venv_10.0/lib64/python3.6/site-packages/dcmstack/extract.py", line 504, in call
value = self._get_elem_value(elem)
File "/<shortened_path>/heudiconv_venv_10.0/lib64/python3.6/site-packages/dcmstack/extract.py", line 423, in _get_elem_value
value = [self.conversionselem.VR for val in value]
TypeError: 'NoneType' object is not iterable

[marlietandoc]

Did you ever end up figuring out if this was a problem? I get the exact same error.

[yarikoptic]

there might have been some fixes in dcmstack since then e.g. moloney/dcmstack#76 . What is the version of dcmstack you have @marlietandoc - do you know? if before 0.9 -- could you try with 0.9?

[marlietandoc]

@yarikoptic Thanks for looking into this. I am using the most up-to-date version of heudiconv (version 0.11.6, running it as a singularity container) I'm trying to verify now what version of dcmstack it is using, but assume its most up to date one?

The exact error I get (for every .json file/scan that Heudiconv tries to create, so its happening every time for all subjects) is as follows:

Node] Error on "embedder" (/tmp/embedmetaxgkuj2qa/embedder)
WARNING: [Node] Error on "embedder" (/tmp/embedmetaxgkuj2qa/embedder)
ERROR: Embedding failed: Exception raised while executing Node embedder.

Traceback (most recent call last):
File "/opt/miniconda-latest/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/opt/miniconda-latest/lib/python3.7/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
out = function_handle(**args)
File "", line 28, in embed_dicom_and_nifti_metadata
File "/opt/miniconda-latest/lib/python3.7/site-packages/dcmstack/dcmstack.py", line 1223, in parse_and_stack
warn_on_except)
File "/opt/miniconda-latest/lib/python3.7/site-packages/dcmstack/dcmstack.py", line 1126, in parse_and_group
meta = extractor(dcm)
File "/opt/miniconda-latest/lib/python3.7/site-packages/dcmstack/extract.py", line 504, in call
value = self._get_elem_value(elem)
File "/opt/miniconda-latest/lib/python3.7/site-packages/dcmstack/extract.py", line 423, in _get_elem_value
value = [self.conversionselem.VR for val in value]
TypeError: 'NoneType' object is not iterable

My main question is just whether or not this is worrisome or not for my preprocessing pipeline further down the road.

[bpinsard]

Got the same error on GE data.
Might be caused by an anonymization tool.

see moloney/dcmstack#93 for potential fix.