mriconvert: Support for exporting BIDS compatible JSON files

[Chris Filo Gorgolewski]

Hi Roman,
Thank you for you feedback. Could you elaborate a bit more why do you
consider command lines producing more than one file so dangerous?

Best,
Chris

On Fri, Oct 2, 2015 at 8:00 PM, Roman Fleysher <
roman.fleysher at einstein.yu.edu> wrote:

> Dear MRIConvert developers,
> Dear MRIConvert users,
>
> I am strictly against such addition to MRIConvert. This functionality must
> be implemented in a separate command. There are other parameters that might
> be needed and other ways to get them. I consider producing such files as
> part of DICOM to NIFTI conversion a side effect. As we know in programming,
> side effects is one of the biggest causes of errors. User interfaces get
> clumsy. Please do not add side effects to MRIConvert. Not this, not any
> other.
>
>
> Thank you,
>
> Roman
>
> ------------------------------
> *From:* mriconvert-bounces at lists.uoregon.edu [
> mriconvert-bounces at lists.uoregon.edu] on behalf of Chris Filo Gorgolewski
> [krzysztof.gorgolewski at gmail.com]
> *Sent:* Friday, October 02, 2015 9:26 PM
> *To:* mriconvert at lists.uoregon.edu
> *Subject:* mriconvert: Support for exporting BIDS compatible JSON files
>
> 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
>
> _______________________________________________
> mriconvert mailing list
> mriconvert at lists.uoregon.edu
> https://lists-prod.uoregon.edu/mailman/listinfo/mriconvert
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists-prod.uoregon.edu/pipermail/mriconvert/attachments/20151002/6a6c5af0/attachment.html>