Some participants have obvious bright crescent-shaped artifacts in their standard deviation images (the examples above are from two people; both calculated from non-censored frames, after completing the HCP Minimal Preprocessing pipeline). Looking over people and runs (some participants have completed 6 imaging sessions, over months), people have the crescents or not - their presence doesn't vary much with session (scanning day), task, or movement level (apparent or real).
They do, however, vary with encoding direction: appearing in PA phase encoding runs only. Plus, they seem to vary with subject head size, more likely in small-headed people (large-headed people seem more likely to have "ripples", but that's an artifact for another day).
All that (and thanks to conversations with practiCal fMRI and @DataLoreNeuro) gave a hint: these crescents appear to be N/2 ghost artifacts.
Playing with the contrast and looking outside the brain has convinced me that the crescents do align with the edges of ghost artifacts, which I tried to show above. These are from a raw image (the HCP Minimal Preprocessing pipelines mask the brain), so it's hard to see; I can share example NIfTIs if anyone is interested.
So, why do we have the bright ghosts, what should we do about it, and what does that mean for analysis of images we've already collected? Suggestions are welcome! For analysis of existing images, I suspect that these will hurt our signal quality a little: we want the task runs to be comparable, but they're not in people with the crescent: voxels within the crescent areas have quite different tSNR in the PA and AP runs.
Holy crescents, Batman! (We've been watching the 1966 Batman TV series.)
I think we might have the Return of the Inadequate Fat Saturation episode afoot:
ReplyDeletehttps://practicalfmri.blogspot.com/2012/12/inadequate-fat-suppression-for.html
So far, everything seen is consistent with scalp ghosts. The PA vs AP visibility is due to the location of the ghosts, i.e. whether they overlap the brain or fall outside the head (or on a non-brain structure of no interest). I'm going to run with this hypothesis and try to devise an experimental proof. Time to pull out my Ziploc bag and olive oil.
I didn't mention it in the post, but I *do* see opposite crescents in the back of the brain in AP runs in a very few people, and these are people with really bright PA crescents.
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ReplyDeleteMy thoughts are similar to Ben's on this. I see these sort of crescents on our ASL images (which have fat sat off by default) on a Philips system. It's not really an issue with the ASL as they cancel out in the control - tag subtraction (usually). I have tried with fat sat on and they go away in our case. Hope you get it sorted out. These sort of things can be really annoying.
ReplyDeleteI've not tried the "MB dual kernel" option on CMRR's MB sequence yet, but according to speedy literature reading, it should reduce the propagation of ghosts from SBRef to the time series by generating separate recon kernel for the odd and even k-space lines. Might help here. I'll test it as soon as I can, most likely the week of 29th.
ReplyDeleteI checked, and we have "MB dual kernel" Off in our functional sequences, so that's now on the list of things to compare. It'll be a few weeks yet before we can test anything, but I'm going to review lab members' scans to see if any have good "crescent" artifacts to be our test people.
DeleteAny news on the "crescent" artifact, and does the "MB dual kernel" option help to prevent the artifact?
DeleteThanks in advance!