This is one of those occurrences (artifacts?) that is difficult to google, but perhaps someone will recognize it or have a guess.
This run is from a session in which a person completed four fMRI runs of a task sequentially. They did not get out of the scanner between these runs, nothing was changed in the protocol, no one entered the scanner room. Later participants (with the same protocol, scanner, etc.), have been fine. This study uses CMRR MB4 acquisitions, so we have an SBRef image for each run; the artifact is the same in the SBRef and functional run.
Runs 1 (not shown), 2, and 4 are normal, but run 3 is much darker than the others and has an obvious ghost-ish artifact, here are the DICOMs from each run's SBRef, allowing mango to adjust the contrast in each:
And here they are again, with contrast set to 1-15000 in all three images:
The functional run's DICOMs are also dark and have the prominent artifact; here's a frame:
When the run is viewed as a movie in mango the blood flow, small head movements, etc. are plainly and typically visible. The artifact does not appreciably shift or change over the course of the run, other than appearing to follow the (small) overt head motions (when the head nodded a bit, the artifact shifted in approximately the same way). The two surrounding runs (2 & 4) are typical in all frames (no sign of the artifact).
Given that this artifact is in the DICOMs, it's not introduced by preprocessing, and I am assuming this run is unusable. I'd like an explanation, though, if nothing else, so we can take any steps to reduce the chance of a recurrence. Our best guess at this time is some sort of transient machine fault, but that's not an especially satisfactory explanation.
Any ideas? Thanks!
update 13 July 2022:
In response to Ben and Renzo's suggestions, I skimmed through the DICOM headers for fields with large differences between the three runs; if there are particular fields to look for, please let me know (this is a Siemens Prisma); I am not fluent in DICOM header! The most obvious are these, which I believe are related to color intensity, but I'm not sure if it's reporting a setting or something determined from the image after it was acquired.
run 2 (typical)
(0028,0107) Largest Image Pixel Value 32238
(0028,1050) Window Center 7579
(0028,1051) Window Width 16269
(0028,1055) Window Center & Width Explanation Algo1
run 3 (dark/artifact)
(0028,0107) Largest Image Pixel Value 3229
(0028,1050) Window Center 1218
(0028,1051) Window Width 3298
(0028,1055) Window Center & Width Explanation Algo1
run 4 (typical)
(0028,0107) Largest Image Pixel Value 31787
(0028,1050) Window Center 7423
(0028,1051) Window Width 15912
(0028,1055) Window Center & Width Explanation Algo1
And here's yet another view from the three functional runs, in which I played with the contrast a bit. There's definitely a difference in which structures are brightest between the three.
Hi Jo, the bright ring artifact visible over the brain is from the scalp fat and indicates that the fat suppression pulse was misbehaving. Then, given that the overall images are dark, too, there is the strong suggestion that the RF excitation pulse was also misbehaving. A simple explanation for both phenomena is some sort of erroneous scaling. Usually the transmitter gain for any RF pulse is set based on a calibration step (the current transmitter voltage), usually done invisibly at session start. If that value was corrupted for one entire run - say, it was suddenly reduced by 90% - then all RF pulses would be made weaker. This would lead to ineffective fat suppression and darker images. It would have to be a big factor; 90% or more, probably.
ReplyDeleteGiven that you say the effect was constant for an entire run, my suspicion falls on the software or possibly operator error. It's not inconceivable as a hardware error, but it's harder to reconcile with good runs before and after. I'm wondering if either the transmitter reference voltage was saved with a low value for the bum run, or if someone accidentally reset the Tx voltage (in the System tab) for just that run. You may be able to query the transmitter voltage in the DICOM header. If not, pulling one of the DICOMs back onto the scanner and dragging it into the exam queue should reveal what the Tx voltage was.
If it happens again and it really hits randomly then you might ask your service engineer to check the RF amplifier in case an attenuator board is getting flaky. But flaky boards tend to produce more intermittent effects. Something affecting one entire scan consistently, and not the scans before or after, that's more likely control/software.
Thanks for the thoughts! I'll look at the headers and investigate further.
DeleteThats a cool artifact, thanks for sharing. I have never seen such an artifact in my own data. However, I think that it could be explained if something went wrong during the frequency adjust, which is usually done at the beginning of each run. This could result in an insufficient fat-saturation pulse and weaker excitation pulse?- Renzo Huber
ReplyDeleteActually, there may be a simpler explanation: motion. There are two things that suggest motion. First, note that the problem image has highest SNR in the occipital region, the opposite of the normal images where frontal lobe is hottest. Second, there is an increased distortion in the frontal region in the problem image. Note the extra stretch at the most anterior portion of the brain, and a small signal "divot" that is not apparent in the normal images. Now we consider why there might be scalp ghosts over the brain. These could result from residual aliasing because of a poor Rx field. All these observations are consistent with the top half of the RF coil being displaced and connected improperly for the duration of the run. I've seen instabilities result from printed head cases (see https://practicalfmri.blogspot.com/2021/02/restraining-32-channel-coil.html) and analogous problems could result from a head very firmly packed in with foam. Given that motion is the usual suspect, I would investigate motion as the most likely cause here, too!
ReplyDeleteWe're not using head cases for this study, but have been seeing more movement than we'd like, and so trying to be more careful with packing; entirely possible this person was quite firmly packed. Reviewing their realignment parameters, they have pretty substantial apparent motion but not that much actual.
DeleteDo you re-shim prior to each run? I'm thinking the motion may actually be between runs, possibly during the pre-scan adjustments (on-res adjustment and shim, if performed). According to your side by side comparisons, there's quite a substantial difference in the absolute brain location between runs #2 and #4. So even if the top half of the coil was performing normally, if the subject moved during a re-shim and the axis of rotation was near the occipital region, we might expect the largest problems in frontal regions.
DeleteAh, this (moving between runs) is quite possible. I will ask whether we re-shim at the start of each run; I don't know. We do regularly advise people that if they must adjust their position to do so between, rather than during runs. We've never seen anything this dramatic before, but have occasionally seen a "dim" run in an otherwise normal session; I will investigate further.
Delete