Adding an OPTIONAL _task-<label> to structural MRI acquisitions?
Melanie Ganz
[Also on GitHub under issue 1177 https://github.com/bids-standard/bids-specification/issues/1177]
Dear all,
I would like some input on the following suggestion. Can we add an OPTIONAL _task- to structural MRI acquisitions as well?
I am currently converting a dataset to be shared in BIDS and can't quite get it all to fit with the available tags for structural MRI.
In my study setup, which is about different prospective and retrospective motion correction techniques for clinical structural MRI acquisitions, I had subjects perform different types of controlled motion (STILL,NOD, SHAKE) during the structural acquisitions.
Besides this I also acquire two conditions, MOCO_ON and MOCO_OFF (meaning prospective motion correction on or off; note, during propsective motion correction the acquired k-space data is changed during acquisition since the actual acquisition is changed). Finally, I can reconstruct the data using extra TRs I tag onto the acquisition or without (_RR).
This leads only for the MPRAGE (I have 5 more sequences) to names like this for the same session(!):
MOCO_OFF_STILL_T1_MPR
MOCO_OFF_STILL_T1_MPR_RR
MOCO_ON_STILL_T1_MPR
MOCO_ON_STILL_T1_MPR_RR
MOCO_OFF_NOD_T1_MPR
MOCO_OFF_NOD_T1_MPR_RR
MOCO_ON_NOD_T1_MPR
MOCO_ON_NOD_T1_MPR_RR
MOCO_OFF_SHAKE_T1_MPR
MOCO_OFF_SHAKE_T1_MPR_RR
MOCO_ON_SHAKE_T1_MPR
MOCO_ON_SHAKE_T1_MPR_RR
Now onto the available labels (from https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#anatomy-imaging-data or even https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html):
_acq-
"This is a custom label the user MAY use to distinguish a different set of parameters used for acquiring the same modality." Now my parameters of the sequence don't change, but the actual sequence does if I consider MOCO ON/OFF a parameter, so I could stuff MOCO_ON/OFF in there.
_ce- - not applicable, contrast doesn't change
_rec-
The only mentioning of motion correction is under the reconstruction _rec-. That makes sense to me in the case of retrospective motion correction, where you have the same k-space data, but reconstruct it differently aka using motion data. Hence, to me the reconstruction label does not cover that I am doing prospective motion (MOCO_ON/OFF). I'll use -acq for this.
Same goes for _RR - by adding extra TRs, I do add stuff to my k-space, so it feels strange to put it under -rec, but it could maybe be used here.
_run-
I could misuse run to now take care of STILL,NOD and SHAKE, but the problem is that I can only sort run numerically.
So here exactly my question comes in. Can we add an OPTIONAL _task- to structural MRI acquisitions as well?
And yes, this is probably a total violation of the 80/20 rule in terms of tasks in sturcturla MRI; my study is quite specific. But looking at the ISMRM MoCo community there's lots of studies out that could be shared and I am trying to make mine an example for that.
Let me know your thoughts!
Kind regards,
Melanie
−−
Yours
sincerely
Melanie Ganz-Benjaminsen
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Direct: + 45 35 45 67 18
Mail: melani...@nru.dk
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Tibor Auer
Hi Melanie,
We are also working on a similar dataset and ran into the same problem as you did. We only had different conditions (still and movement at two levels) and used acq only; however, I also think adding a task field for anatomical images makes sense.
In your case, I would still use a combination of fields, as you described:
- task: still/shake/nod
- acq: pmc/nopmc (for MOCO_ON and MOCO_OFF)
- rec: rr/norr
Also, please, make sure that you do not use any ‘_’ in your field values!
BTW, do you also plan to make your dataset available or is it already?
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
Feladó: 'Melanie Ganz' via bids-discussion <bids-di...@googlegroups.com>
Küldve: 02 August 2022 00:39
Címzett: bids-di...@googlegroups.com
Tárgy: [bids-discussion] Adding an OPTIONAL _task-<label> to structural MRI acquisitions?
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