Education, tips and tricks to help you conduct better fMRI experiments.
Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Thursday, March 13, 2014

WARNING! Stimulation threshold exceeded!

When running fMRI experiments it's not uncommon for the scanner to prohibit what you'd like to do because of a gradient stimulation limit. You may even hit the limit "out of the blue," e.g. when attempting an oblique slice prescription for a scan protocol that has run just fine for you in the past. I'd covered the anisotropy of the gradient stimulation limit as a footnote in an old post on coronal and sagittal fMRI, but it's an issue that causes untold stress and confusion when it happens so I decided to make a dedicated post.

Some of the following is take from Siemens manuals but the principles apply for all scanners. There may be vendor-specific differences in the way the safety checking is computed, however. Check your scanner manuals for details on the particular implementation of stimulus monitoring on your scanner.

According to Siemens, then:

The scanner monitors the physiological effects of the gradients and prohibits initiating scans that exceed some predefined thresholds. On a Siemens scanner the limits are established according to two models, used simultaneously:

The scanner computes the expected stimulation that will arise from the gradient waveforms in the sequence you are attempting to run. If one or both models suggests that a limit will be exceeded, you get an error message. I'll note here that the scanner also monitors in real time the actual gradients being played out in case some sort of fault occurs with the gradient control.

Flirting with failure

If you try to initiate a scan that is predicted to exceed the SAFE model limits then you will get a warning:

Clicking OK starts the scan by informing the safety monitor to change from "normal mode" to a "first level" mode. The scan is still below the legal threshold for dB/dt. From your perspective there's really no difference from a scan that initiates without the warning, but it's prudent to be aware that a subject who hasn't complained of sensations thus far might be about to report feeling something. (See Note 1.) For this reason, you should have ensured during setup that the subject doesn't have his feet crossed or his hands together because either of these body positions creates big "pickup" loops for the switching magnetic fields.

An attempt to exceed the legal limits for dB/dt, established in the "first level" mode, causes a hard failure, indicated by this unequivocal message:

You can cancel the scan, or you can let the scanner compute parameters that will get the stimulation limit back below the dB/dt threshold (Calculate option), or you can reopen the protocol and try to figure out which parameter(s) to change in order to get the scan to run. This is where things get interesting.

As a general rule - and especially when running EPI for fMRI - any change to your acquisition parameters is ill-advised without full consideration of the consequences! Standard procedure in a scientific experiment is to use fixed acquisition parameters. So, before proceeding we need to consider in more detail why the failure occurred. Is it a consistent failure, or is it the first time this particular scan has failed to run in spite of having been used successfully on umpteen prior subjects? If the failure is consistent regardless of subject (or phantom) then you clearly need to change something to render the scan usable under any circumstances. Such a situation is common when you're using a new sequence for the first time and you don't yet know how fast you can go. You will probably need to talk to your support physicist to get more insight.

With EPI in particular, you may be prohibited from scanning for some slice prescriptions while others are perfectly acceptable; a classic "intermittent" failure. Why should this be?

Stimulus limits are ansiotropic

The amount of current induced in the subject's (electrically conductive) body is proportional to the cross-sectional area in the plane perpendicular to the switched gradient direction. Given that the largest, fastest-switched gradient for EPI is the read (or frequency encode) gradient then it's this gradient that is of prime concern for the stimulus limit. And, once the slice selection direction is established - by virtue of your slice prescription - it leaves just two options for the read gradient direction, the other axis becoming the phase-encoded axis by default.

In understanding the safety limits for switched gradients it is useful to consider the body's three planes as if they act like pick-up coils, that is, loops of wire that can sense changing magnetic fields by having an electric current induced in them. Consider this cartoon showing the effective current loops formed in a subject's body when a gradient is switched along one of three cardinal axes (in each case the switched gradient axis is perpendicular to the plane of your screen, and to the black loops in the figures):

The relative areas of effective current loops (in black) produced by gradient switching. An effective current loop is induced in the plane perpendicular to the switched gradient axis. The three principal switched gradient axes are anterior-posterior (A-P), left-right (L-R) and head-foot (H-F), corresponding to effective current loops in the subject's coronal, sagittal and axial planes, respectively.

So let's consider our options for a coronal EPI slice prescription. For coronal slices the slice selection axis is along the subject's A-P direction (which is the Y axis of the magnet for you physicist types). We can use either H-F or L-R for the read gradient direction in the image plane. Now, according to the above cartoon, the body's cross-sectional area in the plane perpendicular to the H-F axis, i.e. the subject's axial plane, is smaller than the cross-sectional area in the plane perpendicular to the L-R axis, i.e. the subject's sagittal plane. (I'm comparing H-F switching to L-R switching in the cartoon, and H-F switching invokes a smaller effective current loop.) Thus, for a fixed read gradient amplitude and switching speed, the induced currents in the subject will be lower if we choose H-F for the read gradient direction instead of L-R. (This assumes, as is virtually always the case for conventional fMRI, that the read gradient is larger than the phase encoding gradient.) We could use L-R for the read axis (along with H-F for phase encoding), but we are going to run into a stimulus limit at a lower read gradient strength (or speed) than if we use H-F for the read gradient.

That's coronal slices dealt with. A quick glance at the cartoon reveals the preferred read gradient axes for the other two cardinal slice prescriptions. For axial slices, the preferred read gradient direction is L-R, making the phase encode axis A-P. For sagittal slices the preferred read gradient direction is H-F, making the phase encode axis A-P as well.

And now for the intermittent behavior. As you tilt an axial slice prescription towards coronal, at some point the scanner transitions from considering your slices as axial obliques to being coronal obliques instead, and it changes the gradient priority according to the previous assignment. Axial slices use L-R for the read gradient by preference, whereas coronal slices use H-F. It is this transition that can trigger the stimulus limit for no "apparent" reason. You may be able to change the slice tilt back towards axial and get back under the limit so that the scan will start.

Body position again

You can now see why making big loops with your arms or legs is ill-advised inside an MRI. Even so, some people have different dimensions than others and some people are simply more sensitive to peripheral nerve stimulation (PNS) than others. On a Siemens scanner, at least, the actual subject geometry isn't considered when computing the stimulus limits. Nor is the actual subject's position. It is therefore entirely possible for a subject to experience PNS even when the scanner doesn't issue any sort of warning. And even if the subject isn't bothered by it, the fact that he's experiencing PNS is likely to be a distraction for whatever fMRI experiment you're running.

In this simple overview I have conveniently neglected the PNS potential of the slice select and phase encode gradients, as well as other gradients that may be active during a scan. For instance, you could be running a thin slice experiment which uses very large, fast-switched slice select gradients. These might be felt by a subject even when the read gradient (for EPI) isn't causing an issue. Finally, give a thought to non-fMRI scans that might trigger a problem for the subject, perhaps requiring early termination of a session before you've obtained all the data you need.

Key points to take away

  • Don't allow subjects to link their arms or feet and make large loops.
  • If a subject reports feeling PNS in his arms, shoulders or legs, see if you can reduce the sensation by moving the pertinent body part farther away from the magnet bore. Padding to keep a subject's arms off the bore may help here, for example.
  • Be aware of your slice prescription and ensure in pilot testing that tilting "too far" won't trigger a stimulus limit issue due to changed default gradient ordering.
  • On a Siemens scanner the stimulus monitor doesn't track the actual subject size or body position, it relies on predefined models.



1.  For fMRI studies, I don't recommend actually informing the subject that he might feel peripheral nerve stimulation during the upcoming scan. There is nothing quite like priming an fMRI subject for behavior you probably don't want! Instead, always ask the subject to squeeze the ball if she feels anything she doesn't like. You should already have briefed your subject on the common sensations - loud noise and vibrations - so you want to know if something changes and/or becomes uncomfortable. The better you have briefed your subject beforehand - a mock scanner with sounds is really useful here - then the easier you will get only correct positive feedback for PNS.

No comments:

Post a Comment