[Neuroimaging] JSON-LD and DICOM?

Satrajit Ghosh satra at mit.edu
Tue Jul 4 11:49:08 EDT 2017

hi matthew,

> > they are being transitioned off to scicrunch/interlex and i'm sure karl
> and
> > i can put together a basic context for us.
> That would be very useful indeed.  Any idea of a time scale for that?

let me talk to karl. this should be doable by middle of next week if not

> Right - or, as you noted in the current JSON header draft, we can make
> ``dcm`` a prefix with its own context, within the context for the JSON
> header extension:
> "@context": "http://nipy.org/nibabel/jhe-context.jsonld"
> where jhe-context.jsonld contains:
>          "@context": {
>             "dcm": "http://nipy.org/nibabel/dicom-context.jsonld"
>           },
> and the JSON header goes something like:
> "@context": "http://nipy.org/nibabel/jhe-context.jsonld",
> "nipy_header_version": "1.0",
> "dcm:Echo_Time": 45,
> etc.

sounds good to me. for the non dicom terms we should describe them in a
context with descriptions and data types as well.

> > e. a view of information that reduces cognitive load
> >
> > as algorithm developers we care about the view, the minimal set of
> > information that is needed to write a function/solve a problem. nifti-1
> was
> > an agglomeration of those views when it was created, together with some
> > backward compatibility decisions with analyze. people were not thinking
> of
> > large databases, diffusion imaging, and other areas that we now consider
> > important. and hence nifti is a view of the underlying information that
> is
> > already out of date. yes the extensions were part of the solution, but
> how
> > many people use the diffusion extension over bvecs and bval files (a la
> > FSL)?
> I think that is partly because of the relative opacity of the
> extension formats.  Even a small binary format needs some software in
> your language to unpack it in a reliable way.  Because it takes this
> work to look at the information, people often don't bother to check if
> the information is what they want, and just throw it away.  That's the
> big advantage of text files and text formats - they can just open the
> file in text editor to have a look if the information is useful.

aren't all data binary on a computer :) ? less/more/cat are programs as
well. it's just that there are many text readers/writers available on most
platforms. i particularly like the following paragraph from this site (

"Computer science is all about creating good abstractions. Sometimes it
succeeds and sometimes it doesn't. Good abstractions are all about
presenting a view of the world that the user can use. One of the most
successful abstractions is the text editor."

if something like nib-ls was readily available and parsed these data and
perhaps allowed editing it easily, i think most people would be happy with


will point you to the context as soon as karl and i have had a chance to
chat and create a version.


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