FileDataset object has no attribute ContentDate

[araikes]

Summary

convertall.txt

I am attempting to use Heudiconv to convert an older dataset in our lab. All sequences were run on a Siemens TrioTim. When running (heuristic attached), I get the following error:

docker run --rm -it -v ${PWD}:/base nipy/heudiconv:0.5.4 -d /base/source/{subject}/{session}/*/*.dcm -o /base/nifti -f /base/code/convertall.py -s 002 -ss bline -c dcm2niix -b --minmeta --overwrite
INFO: Running heudiconv version 0.5.4
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': '002', 'outdir': '/base/nifti/', 'session': 'bline'}
INFO: Processing 2511 dicoms
INFO: Analyzing 2511 dicoms
/src/heudiconv/heudiconv/dicoms.py:58: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment
Please use with caution.  We would be grateful for your help in improving them
  import nibabel.nicom.dicomwrappers as dw
INFO: Generated sequence info with 22 entries
INFO: Doing conversion using dcm2niix
INFO: Converting /base/nifti/sub-HarvBL002/ses-bline/anat/sub-HarvBL002_ses-bline_run-001_T1w (176 DICOMs) -> /base/nifti/sub-HarvBL002/ses-bline/anat . Converter: dcm2niix . Output types: ('nii.gz',)
190430-22:41:09,488 nipype.workflow INFO:
         [Node] Setting-up "convert" in "/tmp/dcm2niixidnhkk01/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixidnhkk01/convert".
190430-22:41:09,525 nipype.workflow INFO:
         [Node] Running "convert" ("nipype.interfaces.dcm2nii.Dcm2niix"), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f anat -o . -s n -v n /tmp/dcm2niixidnhkk01/convert
INFO: [Node] Running "convert" ("nipype.interfaces.dcm2nii.Dcm2niix"), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f anat -o . -s n -v n /tmp/dcm2niixidnhkk01/convert
190430-22:41:10,617 nipype.interface INFO:
         stdout 2019-04-30T22:41:10.616984:Chris Rorden's dcm2niiX version v1.0.20190410  GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-04-30T22:41:10.616984:Chris Rorden's dcm2niiX version v1.0.20190410  GCC6.3.0 (64-bit Linux)
190430-22:41:10,617 nipype.interface INFO:
         stdout 2019-04-30T22:41:10.616984:Found 176 DICOM file(s)
INFO: stdout 2019-04-30T22:41:10.616984:Found 176 DICOM file(s)
190430-22:41:10,617 nipype.interface INFO:
         stdout 2019-04-30T22:41:10.616984:Convert 176 DICOM as ./anat (256x256x176x1)
INFO: stdout 2019-04-30T22:41:10.616984:Convert 176 DICOM as ./anat (256x256x176x1)
190430-22:41:10,844 nipype.interface INFO:
         stdout 2019-04-30T22:41:10.844483:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "./anat.nii"
INFO: stdout 2019-04-30T22:41:10.844483:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "./anat.nii"
190430-22:41:10,844 nipype.interface INFO:
         stdout 2019-04-30T22:41:10.844483:Conversion required 1.246532 seconds (0.354787 for core code).
INFO: stdout 2019-04-30T22:41:10.844483:Conversion required 1.246532 seconds (0.354787 for core code).
190430-22:41:10,872 nipype.workflow INFO:
         [Node] Finished "convert".
INFO: [Node] Finished "convert".
WARNING: Failed to get date/time for the content: 'FileDataset' object has no attribute 'ContentDate'
190430-22:41:14,427 nipype.workflow INFO:
         [Node] Setting-up "embedder" in "/tmp/embedmetauhj0355v/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetauhj0355v/embedder".
190430-22:41:14,456 nipype.workflow INFO:
         [Node] Running "embedder" ("nipype.interfaces.utility.wrappers.Function")
INFO: [Node] Running "embedder" ("nipype.interfaces.utility.wrappers.Function")
190430-22:41:14,466 nipype.workflow INFO:
         [Node] Finished "embedder".
INFO: [Node] Finished "embedder".
INFO: Post-treating /base/nifti/sub-HarvBL002/ses-bline/anat/sub-HarvBL002_ses-bline_run-001_T1w.json file
INFO: Converting /base/nifti/sub-HarvBL002/ses-bline/anat/sub-HarvBL002_ses-bline_run-002_T1w (176 DICOMs) -> /base/nifti/sub-HarvBL002/ses-bline/anat . Converter: dcm2niix . Output types: ('nii.gz',)
190430-22:41:14,500 nipype.workflow INFO:
         [Node] Setting-up "convert" in "/tmp/dcm2niixui0ce2ku/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixui0ce2ku/convert".
190430-22:41:14,541 nipype.workflow INFO:
         [Node] Running "convert" ("nipype.interfaces.dcm2nii.Dcm2niix"), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f anat -o . -s n -v n /tmp/dcm2niixui0ce2ku/convert
INFO: [Node] Running "convert" ("nipype.interfaces.dcm2nii.Dcm2niix"), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f anat -o . -s n -v n /tmp/dcm2niixui0ce2ku/convert
190430-22:41:15,548 nipype.interface INFO:
         stdout 2019-04-30T22:41:15.548758:Chris Rorden's dcm2niiX version v1.0.20190410  GCC6.3.0 (64-bit Linux)
INFO: stdout 2019-04-30T22:41:15.548758:Chris Rorden's dcm2niiX version v1.0.20190410  GCC6.3.0 (64-bit Linux)
190430-22:41:15,549 nipype.interface INFO:
         stdout 2019-04-30T22:41:15.548758:Found 176 DICOM file(s)
INFO: stdout 2019-04-30T22:41:15.548758:Found 176 DICOM file(s)
190430-22:41:15,549 nipype.interface INFO:
         stdout 2019-04-30T22:41:15.548758:Convert 176 DICOM as ./anat (256x256x176x1)
INFO: stdout 2019-04-30T22:41:15.548758:Convert 176 DICOM as ./anat (256x256x176x1)
190430-22:41:15,795 nipype.interface INFO:
         stdout 2019-04-30T22:41:15.795429:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "./anat.nii"
INFO: stdout 2019-04-30T22:41:15.795429:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "./anat.nii"
190430-22:41:15,795 nipype.interface INFO:
         stdout 2019-04-30T22:41:15.795429:Conversion required 1.229756 seconds (0.356964 for core code).
INFO: stdout 2019-04-30T22:41:15.795429:Conversion required 1.229756 seconds (0.356964 for core code).
190430-22:41:15,831 nipype.workflow INFO:
         [Node] Finished "convert".
INFO: [Node] Finished "convert".
WARNING: Failed to get date/time for the content: 'FileDataset' object has no attribute 'ContentDate'
Traceback (most recent call last):
  File "/opt/miniconda-latest/bin/heudiconv", line 11, in <module>
    load_entry_point('heudiconv', 'console_scripts', 'heudiconv')()
  File "/src/heudiconv/heudiconv/cli/run.py", line 127, in main
    process_args(args)
  File "/src/heudiconv/heudiconv/cli/run.py", line 323, in process_args
    dcmconfig=args.dcmconfig,)
  File "/src/heudiconv/heudiconv/convert.py", line 199, in prep_conversion
    dcmconfig=dcmconfig,)
  File "/src/heudiconv/heudiconv/convert.py", line 292, in convert
    save_scans_key(item, bids_outfiles)
  File "/src/heudiconv/heudiconv/bids.py", line 309, in save_scans_key
    op.join(output_dir, 'sub-{0}{1}_scans.tsv'.format(subj, ses)), rows)
  File "/src/heudiconv/heudiconv/bids.py", line 342, in add_rows_to_scans_keys_file
    data_rows_sorted = sorted(data_rows, key=lambda x: (x[1], x[0]))
TypeError: '<' not supported between instances of 'NoneType' and 'str'

It's fine creating the images and jsons for this image. However, it fails out and doesn't continue processing the func/dwi/fmap files. This happens for all of my participants (n =32 x 2 sessions)

Any help would be appreciated.

Thanks

Platform details:

Choose one:

• Local environment

• [ x] Container

nipy/heudiconv:0.5.4

• Heudiconv version:

[mgxd]

@araikes I was able to confirm the bug - I've submitted a fix for it.

Once it's merged, the updated code will be available in the nipy/heudiconv:unstable container