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curate dcmstack extracted metadata

Open mgxd opened this issue 5 years ago • 1 comments

Unsure if this is a problem with the scanner / protocol / extraction, but we should ensure heudiconv output does not produce illegal JSON

related issue - https://neurostars.org/t/error-with-node-split-using-fmriprep-distortion-correction-with-fieldmap-data/6039

mgxd avatar Feb 12 '20 16:02 mgxd

isn't

 File "/usr/local/miniconda/lib/python3.7/genericpath.py", line 30, in isfile
 st = os.stat(path)
 ValueError: embedded null byte

suggesting that it is null byte in the filename and has nothing to do with the content of the file? or that is irrelevant traceback from nipype?

Also

 I’ve converted raw DICOM to NIFTI using HeuDiConv and manually inputed ‘IntendedFor’: 
 [‘path/to/file,’ ‘path/to/file2’, …] in each phasediff.json file. All subject directories passed bids 
 validation.

That may be smth could have been "ruined" by that "manual" step?

Most obvious suspect could have been json_dumps_pretty but that one falls back to regular json.dumps if reloaded file anyhow differs.

So I am not yet sure if whatever the problem there is, it is caused by heudiconv per se

yarikoptic avatar Feb 12 '20 17:02 yarikoptic