[Neuroimaging] JSON-LD and DICOM?

[David Gutman]

Just to chime in briefly.. one thing that wasn't mentioned re: DICOM is the
fact of potential PHI leaks.    Ensuring any and all DICOM tags have no PHI
in it is an incredibly tedious/expensive undertaking, and at least for
those of us who use clinical scans for some of our work, the overhead of
trying to make sure we truly anonymized everything in the DICOM header is
significant.

Whereas in the case of NIFTI, as long as the filename doesn't contain the
embedded patient name , I can be pretty sure the files are "clean".

This is particularly important when grad students are working on their own
laptops which are... not particularly secure.




On Tue, Jul 4, 2017 at 1:01 PM Chris Gorgolewski <
krzysztof.gorgolewski at gmail.com> wrote:

> I wonder if in the future it would also make sense to:
>
> 1) add option of creating sidecar BIDS compatible JSON files into nibabel
> (similar to what dcm2niix, dicm2nii, and mcverter are doing). This makes
> some sense since nibabel will become a dicom to nifti converter after
> dcmstack is merged.
>
> 2) store the same content in the header (for "future" compatibility) under
> a different namespace than "dcm" (would that work Satra? How would an
> example JSON-LD with both "dcm" and "bids" look like?)
>
> Not a huge priority, but something to think about. I am very glad that
> dcmstack is getting merged into nibabel.
>
> Best,
> Chris
>
> On Tue, Jul 4, 2017 at 12:47 PM, Satrajit Ghosh <satra at mit.edu> wrote:
>
>> Excellent - that would be very helpful.  Will y'all be able to define
>>> the @types as well as the @ids ?  I guess that would be a lot more
>>> work.
>>>
>>
>> it shouldn't be too hard to combine it with this:
>>
>> https://github.com/pydicom/pydicom/blob/master/pydicom/_dicom_dict.py
>>
>> which itself is generated from the dicom standard and private
>> dictionaries (these are not in karl's curation though and likely varies by
>> sequence and scanner software versions).
>>
>> https://github.com/pydicom/pydicom/tree/master/source/generate_dict
>>
>> cheers,
>>
>> satra
>>
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-- 
David A Gutman MD PhD
Assistant Professor of Neurology, Psychiatry & Biomedical Informatics
Emory University School of Medicine
Staff Physician, Mental Health Service Line
Atlanta VA Medical Center
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