[Neuroimaging] JSON-LD and DICOM?

[valabregue]

On 07/03/2017 11:54 AM, Matthew Brett wrote:
> 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.
Well may be it is not a big deal to make both possible ... ?

It looks like nifti files extension  img+hdf or .nii
well I agree with you: all in once is more obvious. ( like for nifti 
file I prefer the .nii files). The only disadvantage I see is that you 
may loose some nifti compatibility with other software that expect only 
a fix header. (345 byte). So depending on what you plan to do, both may 
be chosen.


Romain