[Neuroimaging] JSON-LD and DICOM?

[Reid, Robert I. (Rob)]

Fortunately nifti header extensions are very easy to remove, either explicitly with nibabel or nifti_tool, or accidentally with FSL.

     Rob

-- 
Robert I. Reid, Ph.D. | Sr. Analyst/Programmer, Information Technology
Aging and Dementia Imaging Research | Opus Center for Advanced Imaging Research
Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org


-----Original Message-----
From: Neuroimaging [mailto:neuroimaging-bounces+reid.robert=mayo.edu at python.org] On Behalf Of Bennet Fauber
Sent: Tuesday, July 04, 2017 12:17 PM
To: Neuroimaging analysis in Python
Subject: Re: [Neuroimaging] JSON-LD and DICOM?

Oh, yes.  That is very important.

Converting to .nii is one of our main ways of insuring no leakage of any subject information -- not just PHI, but potentially names and other information about research subject that, while not regulated, would discourteous to expose.




On Tue, Jul 4, 2017 at 1:05 PM, David Gutman <dagutman at gmail.com> wrote:
> 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.p
>>> y
>>>
>>> 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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>>
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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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