[Neuroimaging] JSON-LD and DICOM?

[Matthew Brett]

Hi,

On Mon, Jul 3, 2017 at 9:21 AM, valabregue <romain.valabregue at upmc.fr> wrote:
> Hi all,
>
>
>
> On 06/30/2017 09:57 PM, Matthew Brett wrote:
>>
>> Hi,
>>
>> On Fri, Jun 30, 2017 at 5:35 PM, Jasper van den Bosch <japsai at gmail.com>
>> wrote:
>>>
>>> Hi all,
>>> I have to agree with Andrey on the yet another format argument. Also,
>>> tools
>>> will have to convert it to other formats anyway, so if you do end up
>>> storing
>>> something in the header, as long as you document it, just like you would
>>> other nibabel properties, I'd go for the simplest solution.
>>
>> There is going to be a JSON header extension quite soon, so it's not
>> really another format, but another way of storing metadata in NIfTI.
>> Then the question is - should we also store DICOM metadata there?
>
> Yes we should store the Dicom metadata, this is the less effort, and it
> fulfills the needs ... May be I miss the point. What would be the
> alternative ? (to define a new ontologie for the metadata ?)
>
> I am using (since a couple a years) the dcmstack that convert dicom to nifti
> + a json file (with all dicom meta data AND more importantly all private
> siemens fields). The nice feature of this conversion is that it aggregates
> field that are identical in all split dicom file (and keep array only when
> it is necessary).
>
> Why not use this solution ?

Actually, the reason I'm interested in this now is because I am
thinking about how to integrate dcmstack into nibabel.  So I wanted to
fuse the dcmstack metadata analysis into the NIfTI header.

> I do not see any clear advantage to have this meta data information directly
> in the nifti file (a naming convention make it easy to keep a link)

Well - let's say there are two options:

* A NIfTI file with a JSON header, where the JSON header contains the
DICOM metadata;
* A NIfTI file with a JSON header, where the the DICOM metadata is in
a separate JSON file.

To me the first seems more obvious than the second.  Surely it also
makes things like provenance just a little bit easier - because it is
just a little bit harder to lose the relationship between the image
and the metadata.

Cheers,

Matthew