This is a cross-post from here. Some of the field map sequences (
RB1map) in the qMRI BIDS documentation (BEP001) are unspecified in terms of how many images BIDS expects and what their required metadata should be.
For example, the paper detailing the
TB1SRGE sequence seems to suggest two images output by the scanner, one for each flip angle. However, this isn’t in the documentation, presumably because these are relatively new imaging sequences. I was wondering if anyone has knowledge of these sequences and how they should be organized to be BIDS-compliant.
As I suggested coming here, I feel a bit obligated to try to direct attention. Created the qmri tag to hopefully help ensure these topics are findable. Will tag in @agahkarakuzu @Gilles_de_Hollander as a first pass, though I’m sure there are others who could respond equally well.
Hey @dlevitas thank you for reaching out!
RB1map, these are derived from file collecitons such as
TB1SRGE. You can see metadata requirements for qMRI maps for the metadata expected for these
TB1DAM has a simpler use case, something like:
This table specifices that the
flip entity is required.
TB1SRGE): The method is nearly 9 years old, but as it is a WIP sequence, not commonly accessible. We did not have an example dataset for SA2RAGE, but the use case was added based on the method descriptions. This one actually calls for using
acq keyword to describe two images with two
DelayTime(s), something like:
I agree that adding these for all fmap file collections would be more useful. @effigies should I open a PR for this?
I think fleshing out the spec is always a good idea. I would be curious to hear from @dlevitas (or anybody else with similar questions) about what would help make these questions easier to find answers for; I worry that those of us who spend so much time around the spec may not see the hurdles clearly.
Thanks @agahkarakuzu, that helped a lot! What confused me was that even though the table is available, not all field map sequences have a table like this:
├── sub-01_echo-1_flip-1_TB1EPI.nii.gz (SE)
├── sub-01_echo-2_flip-1_TB1EPI.nii.gz (STE)
├── sub-01_echo-1_flip-2_TB1EPI.nii.gz (SE)
├── sub-01_echo-2_flip-2_TB1EPI.nii.gz (STE)
I personally finds these the most useful, as they inform the reader of the specific entity labels required (or recommended). There isn’t a table like this for
TB1SRGE, which is why I wanted to clarify. Though I suppose it’s a moot point since the sequence is WIP.