Open Kevancic opened 1 year ago
Hi @Kevancic,
I noticed that you made a similar post a while back, and have also used information from there in my answer below. As a disclaimer, this is just my opinion as I did not work on the original qMRI-BIDS standard (though I have worked on refactoring the B1 mapping code in the hMRI toolbox).
The file collection you describe is very similar to the double angle mapping (TB1DAM
) approach, however in that case only two flip angles are acquired and it is expected that the flip angles have the specific relationship FA2 = 2*FA1
, as that simplifies the arithmetic. A "quick and dirty" hack would be to use the TB1DAM
suffix but in addition to _flip-1
and _flip-2
also have a _flip-3
to _flip-16
in the fmap
directory. This might pass the BIDS validator if it doesn't check for the number of flip angles. I would expect that software packages would expect the first two angles to have the DAM relationship, and so you may want to order your data in that way if you have e.g. a 30° and a 60° case in your dataset.
However you are correct that the proper way to put this into BIDS is to make a pull request with a new TB1 file collection. This file collection would then include TB1DAM
as a special case. This would require you to work with one of the qMRI-BIDS developers to get it into the standard.
You mentioned in the previous thread that you couldn't find literature on this sort of acquisition. One source could be
Bouhrara, M, Spencer, RG. Steady-state double-angle method for rapid B1 mapping. Magn Reson Med. 2019; 82: 189– 201. https://doi.org/10.1002/mrm.27708
as they include the full steady state equation and a look-up-table rather than assuming complete relaxation between excitations, though they still only use two flip angles.
As an aside (i.e. just out of curiosity, as I don't think these details are relevant to answer your question) there are some aspects of your method that are still unclear to me, specifically:
Best, Luke.
Hi @lukeje !
Thanks, making it look like a double-angle dataset is smart, we'll try that.
For your extra questions:
Thanks again!
Yael
Hi Yaël,
Thanks for the further information; that all makes sense.
Regarding pairs of angles, I was rather wondering what the most optimal way to sample the full dynamic range is. Is equispaced sampling optimal, or would it be better to choose e.g. FA1 = 15°, FA2 = 30°, FA3 = 60°, etc. which simplifies the structure of the estimation problem by reducing it to the estimation of a polynomial in FA1? As you say, though, since you have lots of time ex vivo, there is less need to evaluate what the optimal protocol would be.
We’re trying to organize our ex vivo MRI data into BIDS-compliant format, and are facing issues with our B1+ maps.
We are not using any of the standard B1+ mapping protocols listed in the qMRI appendix and are not sure how to best organize this data. To measure B1, we acquire FLASH images with many different flip angles and a long TR, and fit the bloch equation using a look-up table.
I see three potential ways of organizing this data:
Create a new TB1 file collection (TB1VFA?), but this does not seem to be BIDS-compatible Use one of the standard TB1 suffixes. This feels very wrong. Add them as anatomical VFA data. But I am worried it will confuse users, who will have to differentiate between the actual high-resolution anatomical VFAs, and the low-resolution VFAs used for B1 mapping. Is there a good way to do this?
Thanks!