Outputting auxiliary information

[davecash75]

Hi Pawel-
Since the Nifti format cannot hold information about time frames or the tracer and many modelling software needs that information, would it be possible to create a BIDS sidecar or a SIF file as part of the output to mmrchain so that it would be easier to use these files as inputs into tracer kinetics programs?
Many thanks
David Cash

[jjleewustledu]

Pawel and David: To gather some information regarding time frames and tracer characteristics, I’ve used pydicom and interfile packages in my own methods that call NIPET. Working codes are at: https://github.com/jjleewustledu/NiftyPETy/blob/master/respet/recon/reconstruction.py <https://github.com/jjleewustledu/NiftyPETy/blob/master/respet/recon/reconstruction.py> https://github.com/jjleewustledu/NiftyPETy/blob/master/tests/test_reconstruction.py <https://github.com/jjleewustledu/NiftyPETy/blob/master/tests/test_reconstruction.py> Method createDynamic demonstrates the essential ideas. Please note that these methods are embedded in a rather elaborate scheme for aligning NAC PET frames, registering mu-maps to each NAC frame and then creating AC frames. Only the subset of methods called by createDynamic are likely to be of interest. John

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On May 2, 2019, at 9:56 AM, davecash75 ***@***.***> wrote: Hi Pawel- Since the Nifti format cannot hold information about time frames or the tracer and many modelling software needs that information, would it be possible to create a BIDS sidecar or a SIF file as part of the output to mmrchain so that it would be easier to use these files as inputs into tracer kinetics programs? Many thanks David Cash — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD4SZZ2M6KUYSOGIAQSAIYLPTL6IHANCNFSM4HJ7EQPQ>.

[pjmark]

Dave, this is my plan to use BIDS for this, among other reasons.

John, is your pipeline compatible with BIDS?

Cheers,
Pawel

[jjleewustledu]

Pawel, I’ve not seen many specifications for PET in BIDS and I may be missing significant BIDS requirements. Have you any requirements lists that you advocate? I’ve tried to follow BIDS except for circumstances for which there is a conflict with idioms from XNAT, in which case I use the XNAT idioms. The json information I record is specific to my scheme for registering mu-maps to time-frames. I’ll do a more thorough comparison with BIDS specifications and get back to you. John

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On May 16, 2019, at 1:04 PM, Pawel ***@***.***> wrote: Dave, this is my plan to use BIDS for this, among other reasons. John, is your pipeline compatible with BIDS? Cheers, Pawel — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD4SZZ4UWUAKXPEESDEK5ATPVWO2VANCNFSM4HJ7EQPQ>.

[davecash75]

Hi John-
The BIDS format for PET is indeed a work in progress, so I think some interim decisions about how best to fill in the auxiliary metadata will have to be taken. I think APPIAN has a reasonable looking first stab at what should be included and that is what I have been working to in terms of the information I have been filling in.
@pjmark I see some software that stores the prompts, randoms and trues in order to generate weights for non-linear fitting in kinetic modelling. Is that something that also be added to BIDS?

[jjleewustledu]

Some of my projects may benefit from APPIAN. I’ll fork NIPET and see what I can do. John

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On May 17, 2019, at 05:58, davecash75 ***@***.***> wrote: Hi John- The BIDS format for PET is indeed a work in progress, so I think some interim decisions about how best to fill in the auxiliary metadata will have to be taken. I think APPIAN has a reasonable looking first stab at what should be included and that is what I have been working to in terms of the information I have been filling in. @pjmark I see some software that stores the prompts, randoms and trues in order to generate weights for non-linear fitting in kinetic modelling. Is that something that also be added to BIDS? — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.