I can’t answer all your questions because I’m not an fMRIPrep user, but I can help with the tedana part. First, I see you’re using tedana v0.0.12. That version was released in 2022. I’d recommend updating to the current version (v24.0.1). We’ve made a lot of changes including bug fixes and improvements to tedana’s QC report and outputs of additional information that might help with your QC goals.
Explanations of the figures in tedana report and how to use that information for QC is at: Outputs of tedana — tedana 24.0.1 documentation
On some of your more specific questions:
- I agree that only 10 accepted components is low, but a “good number” might vary depending on the quality and number of volumes in your dataset. I’d suggest first looking at the total number of components. If there are nearly as many components as time points or the total number of components is <1/5 of the number of time points, that’s a known problem we are currently trying to address. The right number of accepted components is trickier because it will vary based on data quality and runs with more structured noise might have fewer accepted components. This is where our interactive reports are useful in that you can look at rejected components to check if they are plausibly rejected.
- TNSR post tedana has limited use. If tedana rejects components, it will reduce the total variance of the data and will always increase TSNR. It’s might be nice to know how much TSNR changes, but it will always go up. If you have task data, you can pick a regions with known response (i.e. primary visual and motor cortices in a visuomotor task) and check if tedana inprove the F or T statistics in those areas.
- With or without tedana, an ideal TSNR threshold depends a lot on your other acquisition parameters and study goals. TSNR=>50 is an ok metric for many fMRI studies, but I’d look more carefully at how much TSNR variance across brain regions and subjects. If you’re getting TSNR>100 in most subjects and one subject is 70, that’s a warning sign.
I might as well self-promote a bit and reference an article I wrote on QC that outlines my perspective a bit more generally (including a list of questions to answer in the appendix ( Frontiers | The art and science of using quality control to understand and improve fMRI data ). That’s part of a special issue on QC which includes perspectives from many groups.
I hope this helps.
Dan