NITRC NIfTI Forum: extending_nifti

JNIfTI - a JSON/binary JSON based format for storing neuroimaging data

Qianqian Fang — Tue, 18 Jun 2019 14:40:07 GMT

hi everyone,

(I previously posted this message on this Github discussion thread, but would love to share it here as well
https://github.com/bids-standard/bids-specification/issues/197#issuecomment-502137331 )

I just want to let everyone know I am currently working on a new neuroimaging data interchange format, called JNIfTI.

My current draft of the file specification can be found at

https://github.com/fangq/jnifti/

together you can find a matlab nifti-1/2 to jnifti converter and jnii/bnii data samples.

https://github.com/fangq/jnifti/blob/master/lib/matlab/
https://github.com/fangq/jnifti/tree/master/samples

The basic idea is to use JSON and binary JSON (UBJSON) format to store complex scientific data, and completely get rid of a rigid, difficult-to-extend binary header. This makes the data readable, easy to extend and mixing with scientific data from other domains (like multi-modal data, physiology recordings, or computational models etc). There are also numerous JSON/UBJSON parsers out there, so, without writing any new code, a JNIfTI file can be readily parsed by these existing codes.

JNIfTI is designed with a compatibility layer to 100% translate the NIFTI-1/2 header/data/extension to the new structure, but once it is moved to JSON, you gain enormous flexibility to add new metadata, header info, organizing multiple datasets inside one document etc. I'd love to hear from this community, what additional information that are current lacking, and happy to accept proposals on defining new "required" metadata headers in to this format. My preference is to gradually shift the main metadata container from the NIFTIHeader structure to the "_DataInfo_" and "Properties" subfields in NIFTIData as the primary containers for metadata. This provides an opportunity to completely redesign the header entries.

https://github.com/fangq/jnifti/blob/master/JNIfTI_specification.md#structure-form

look forward to hearing from you.

PS: The foundation of the JNIfTI format is another specification called JData - a proposal to systematically serialize complex data structures, such as N-D arrays, trees, graphs, linked lists etc. The JData specification is current in Draft 1, and can be found at

https://github.com/fangq/jdata/

RE: Proposed (minor) update for NIFTI sform values

Christopher Markiewicz — Tue, 02 Apr 2019 2:35:02 GMT

Hi all,

Just a note that NIFTI_XFORM_TEMPLATE_OTHER is supported in nibabel 2.4.0+.

Chris

RE: Proposed (minor) update for NIFTI sform values

paul taylor — Mon, 18 Mar 2019 12:52:03 GMT

Hi, Guillaume-

Great, glad that is doable.

Cheers,
pt

RE: Proposed (minor) update for NIFTI sform values

Guillaume Flandin — Mon, 18 Mar 2019 11:48:02 GMT

Hello,

The suggested change looks good to us and we will update the SPM NIfTI library accordingly.

Best,
Guillaume.

RE: Proposed (minor) update for NIFTI sform values

paul taylor — Sat, 16 Mar 2019 20:00:58 GMT

Hi, Mark-

Great, thanks for the comments and glad to know that it seems like a positive idea to you.

And yes, the initial post's phrasing just mentioned the sform_code, but we certainly mean to apply it equivalently to qform_code values, which, as you note, should typically (if not always?) match.

Cheers,
pt

RE: Proposed (minor) update for NIFTI sform values

Mark Jenkinson — Sat, 16 Mar 2019 8:36:35 GMT

I think the new code makes a lot of sense and would be fine with FSL. I'd definitely avoid using the unknown code, as this would cause problems for FSL too. I would support having the code available for qforms too, as it is quite common for users to want both the qform and sform to be the same.

Cheers,
MJ

RE: Proposed (minor) update for NIFTI sform values

Richard Reynolds — Fri, 08 Mar 2019 17:57:01 GMT

Hi Chris,

We were planning to do it soon, now that people have had a chance to voice any concerns. Posting a message to this thread once done might be the only additional announcement.

That path to nifti1.h under AFNI will indeed be updated, though the main NIFTI repository list is now on github under https://github.com/NIFTI-Imaging , where nifti1.h is at https://github.com/NIFTI-Imaging/nifti_clib/blob/master/niftilib/nifti1.h . nifti_clib is its own repo, for example.

Soon we will remove those trees from AFNI.

- rick

RE: Proposed (minor) update for NIFTI sform values

Christopher Markiewicz — Fri, 08 Mar 2019 16:36:09 GMT

Hi Paul, Rick,

What's the timeline and process for this change? I assume it'll show up in https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h once ratified? Will there be other announcements to watch for?

Chris

RE: Proposed (minor) update for NIFTI sform values

doug greve — Fri, 01 Mar 2019 16:06:40 GMT

FreeSurfer does not use this field, so it should have no effect on our code

RE: Proposed (minor) update for NIFTI sform values

Richard Reynolds — Thu, 28 Feb 2019 20:51:20 GMT

Hi Chris,

NIFTI_XFORM_TEMPLATE_OTHER seems like a nice choice.

Yes, this would apply to both qform and sform. We do the same thing with synchronizing them.

- rick