mriconvert: Support for exporting BIDS compatible JSON files

[Chris Filo Gorgolewski]

Dear developers of MRIConvert,

Brain Imaging Data Structure (BIDS)
<https://docs.google.com/document/d/1HFUkAEE-pB-angVcYe6pf_-fVf4sCpOHKesUvfb8Grc/edit#>
is
a new specification describing how a neuroimaging dataset should be
organized and described. Part of the standard are JSON sidecar files with
acquisition parameters essential for performing data analysis that are not
present (or reliably reported) in the NIFTI header (see here
<https://docs.google.com/document/d/1HFUkAEE-pB-angVcYe6pf_-fVf4sCpOHKesUvfb8Grc/edit#heading=h.r8mrcau3kkcq>
for
details). Such fields include but are not limited to:

   - EffectiveEchoSpacing
   - RepetitionTime
   - PhaseEncodingDirection
   - SliceTiming
   - SliceEncodingDirection
   - EchoTime

Some of those fields are part of DICOM Ontology and are directly accessible
from standard DICOM headers (such as RepetitionTime and EchoTime) and some
are not part of standard DICOM nomenclature and require extraction using
vendor and sequence specific heuristics (for example PhaseEncodingDirection
or EffectiveEchoSpacing). We aded them to the BIDS standard because they
are necessary for data processing.

This is how an example BIDS compatible JSON file looks like (more examples
here <https://github.com/INCF/BIDS-examples>):

{
    "EchoTime": 0.017,
    "EffectiveEchoSpacing": 0.0003333262223739227,
    "PhaseEncodingDirection": "y-",
    "RepetitionTime": 3.0,
    "SliceEncodingDirection": "z",
    "SliceTiming": [
        1.508,
        0.0,
        1.55,
        0.043,
        1.592,
        0.087,
        1.635,
        0.13,
        1.677,
        0.173,
        1.722,
        0.215,
        1.765,
        0.26,
        1.808,
        0.302,
        1.85,
        0.345,
        1.893,
        0.388,
        1.938,
        0.43,
        1.98,
        0.475,
        2.022,
        0.518,
        2.065,
        0.56,
        2.11,
        0.603,
        2.152,
        0.645,
        2.195,
        0.69,
        2.238,
        0.733,
        2.28,
        0.775,
        2.325,
        0.818,
        2.367,
        0.86,
        2.41,
        0.905,
        2.453,
        0.948,
        2.495,
        0.99,
        2.54,
        1.032,
        2.583,
        1.075,
        2.625,
        1.12,
        2.668,
        1.163,
        2.71,
        1.205,
        2.755,
        1.248,
        2.798,
        1.293,
        2.84,
        1.335,
        2.883,
        1.378,
        2.925,
        1.42,
        2.97,
        1.462
    ]
}

I've heard a lot of good things about MRIConvert. It would be great if the
future release supported saving BIDS style JSON files along the converted
NIFTI files. In addition you can consider embedding this JSON inside the
header (similar to what dcmstack does). From looking at your code base I
see that you already calculate many of the required parameters. I'm more
than happy to provide any help in implementing this feature.


I have reached out to other developers of DICOM to NIFTI converters with
similar proposals. I hope that soon we will have a common way of describing
NIFTI metadata!


Best regards,

Chris Gorgolewski
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