Summary of what happened:
I’ve downloaded the PARDIP dataset from the NDA repository, and the dicoms were all anonymized prior to being put in the repository. I was able to use heudiconv to pull out a template on a single subject, as a first step, but the dicominfo.tsv file showed the protocol field is ‘anonymous’, the patient id, study description, series description are all ‘anonymous’. The only way to kind of determine what the output nifti file should be called was to look at the sequence_name field. There is an epifid2d1_64 for the resting state, tfl3d1_ns for the T1, *tse2d2_7 for the T2, etc.
I have not successfully used heudiconv before; I got a walkthrough from someone who uses it on their own data so they haven’t dealt with anonymized dicoms. But I worked through their scripts and converted them, to try on the same single subject that I got the dicominfo.tsv file from (running heudiconv with the -c none option, same subject.)
It seems to be working, in that it finds the files, and does actually convert the anatomy and T2 dicoms, puts them in the right place with the right names, etc.
But it doesn’t output the resting state or DTI files–and the output is full of error warnings. I did check that dcm2niix will work by itself on these images, so the error must be something else I’ve done in the heuristic file in trying to get the names and BIDS formats right.
But the error below shows that “Anonymous” is trying to get converted to a float, during the embedder process? Is that an error I need to work around? If I can ignore that I can move on to the other errors.
Command used (and if a helper script was used, a link to the helper script or the command generated):
(the bold and italics is something weird in formatting here; those are all variable names that do actually evaluate properly)
singularity run --cleanenv
/fs/ess/PCON0501/Heudiconv_scripts/heudiconv_latest.sif
–files {dirpath}/{Data}/{subject}_files/*.dcm \
-o {dirpath}/{Study}/Analyses/ \
-f {dirpath}/${Data}/PARDIPheuristic.py
-s $subject
-ss $session
-c dcm2niix
-b
–overwrite ;
Version:
latest --I did the singularity pull command just five days ago.
Environment (Docker, Singularity, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
No it isn’t, that’s the problem.
Relevant log outputs (up to 20 lines):
Starting BIDS conversion for subject S0078JWR 1
INFO: Running heudiconv version 0.13.1 latest 0.13.1
INFO: Analyzing 710 dicoms
INFO: Generated sequence info for 1 studies with 8 entries total
WARNING: Heuristic is missing an infotoids method, assigning empty method and using provided subject id S0078JWR. Provide session and locator fields for best results.
INFO: Study session for StudySessionInfo(locator=None, session=‘1’, subject=‘S0078JWR’)
…
INFO: PROCESSING STARTS: {‘subject’: ‘S0078JWR’, ‘outdir’: ‘/fs/ess/PCON0501/PARDIP/Analyses/’, ‘session’: ‘1’}
INFO: Processing 8 pre-sorted seqinfo entries
INFO: Doing conversion using dcm2niix
…
INFO: [Node] Finished “embedder”, elapsed time 0.018789s.
230830-10:58:38,750 nipype.workflow WARNING:
Storing result file without outputs
WARNING: Storing result file without outputs
230830-10:58:38,751 nipype.workflow WARNING:
[Node] Error on “embedder” (/tmp/embedmetaiobs88ab/embedder)
WARNING: [Node] Error on “embedder” (/tmp/embedmetaiobs88ab/embedder)
ERROR: Embedding failed: Exception raised while executing Node embedder.
Traceback:
Traceback (most recent call last):
File “/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/nipype/interfaces/base/core.py”, line 397, 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 142, in _run_interface
out = function_handle(**args)
File “”, line 35, in embed_dicom_and_nifti_metadata
File “/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/dcmstack/dcmstack.py”, line 1156, in parse_and_stack
results = parse_and_group(src_paths,
File “/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/dcmstack/dcmstack.py”, line 1060, in parse_and_group
meta = extractor(dcm)
File “/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/dcmstack/extract.py”, line 504, in call
value = self._get_elem_value(elem)
File “/opt/miniconda-py39_4.12.0/lib/python3.9/site-packages/dcmstack/extract.py”, line 421, in _get_elem_value
value = self.conversionselem.VR
ValueError: could not convert string to float: ‘Anonymous’
And it ends with:
INFO: stdout 2023-08-30T16:44:06.005821:Conversion required 0.730743 seconds (0.067720 for core code
).
230830-16:44:06,26 nipype.workflow INFO:
[Node] Finished “convert”, elapsed time 0.780368s.
INFO: [Node] Finished “convert”, elapsed time 0.780368s.
Traceback (most recent call last):
File “/opt/miniconda-py39_4.12.0/bin/heudiconv”, line 8, in
sys.exit(main())
File “/src/heudiconv/heudiconv/cli/run.py”, line 30, in main
workflow(**kwargs)
File “/src/heudiconv/heudiconv/main.py”, line 463, in workflow
prep_conversion(
File “/src/heudiconv/heudiconv/convert.py”, line 255, in prep_conversion
convert(
File “/src/heudiconv/heudiconv/convert.py”, line 635, in convert
tuneup_bids_json_files(bids_outfiles)
File “/src/heudiconv/heudiconv/bids.py”, line 334, in tuneup_bids_json_files
assert HEUDICONV_VERSION_JSON_KEY not in json_
AssertionError
Screenshots / relevant information:
LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
(if that is relevant. I’m pretty sure the problem is something about the anonymized dicom tags that I need to set some specific flag for…)
