Motion traces for the respiratory oscillations in EPI and SMS-EPI

This is a follow-up post to Respiratory oscillations in EPI and SMS-EPI. Thanks to Jo Etzel at WashU, you may view here the apparent head motion reported by the realignment algorithm in SPM12 for the experiments described in the previous post. Each time series is 200 volumes long, TR=1000 ms per volume. The realignment algorithm uses the first volume in each series as the template. The motion is plotted in the laboratory frame, where Z is the magnet bore axis (head-to-foot for a supine subject), X is left-right and Y is anterior-posterior for a supine subject.

In the last post I said that there were five total episodes of a deep breath followed by sigh-like exhale, but actually the subject produced a breath-exhale on average every 30 seconds throughout the runs. (This was a self-paced exercise.) Thus, what you see below (and in the prior post) has a rather large degree of behavioral variability. Still, the main points I made previously are confirmed in the motion traces. I'll begin with the axial scan comparison. Here are the motion parameters for the MB=6 axial acquisition with standard foam head restraint (left) versus the custom printed restraint (right):

MB=6, axial slices. Left: foam restraint. Right: custom 3D printed headcase restraint

The effect of the custom restraint is quite clear. The deep breath-then-sigh episodes are especially apparent when using only foam restraint. Note the rather similar appearance of the high frequency oscillations, particularly apparent in the blue (Y axis) traces between the two restraint systems, suggesting that the origin of these fluctuations is B0 modulation from chest motion rather than direct mechanical motion of the head. We cannot yet be sure of this explanation, however, and I am keeping an open mind just in case there are small movements that the custom head restraint doesn't fix.

The product EPI acquisition of axial slices shows a similar benefit of the custom restraint:

Product EPI, axial slices. Left: foam restraint. Right: custom 3D printed headcase restraint

Furthermore, comparing the above two figures we can confirm that the overall motion sensitivity of the SMS acquisition (MB=6) and product EPI is quite similar for both foam and custom restraints, when spatial and temporal parameters are matched (except for total number of slices per TR). In spite of the task variability the peak-to-peak excursions are consistent across the restraint system being used.

I find it interesting that the realignment algorithm reports similar motion for product EPI, with only 11 total slices, as for SMS-EPI with 66 slices. The total anatomical content in the 11 axial slices located at the top of the head is markedly lower than the near full brain coverage of the 66 slice acquisition. Yet there doesn't appear to be a large cost for the poorer coverage. Perhaps there is slightly greater low frequency drift being reported for product EPI than SMS-EPI when using foam padding. The rather similar drifts apparent when using custom restraint would suggest that gradient heating isn't the cause. It's something I will look into in more detail separately, since Jo has kindly re-run the motion correction using a subset of the full SMS-EPI data.


Next I want to consider the coronal comparisons, because we retain the issue of low brain coverage and low anatomical content for the product EPI images. The 11 slices of the product EPI acquisition were positioned over the occipital cortex. Here is the MB=6 coronal acquisition with standard foam head restraint (left) versus the custom printed restraint (right):

MB=6, coronal slices. Left: foam restraint. Right: custom 3D printed headcase restraint

The excursions in pitch (red traces) and yaw (brown traces) in particular, appear to be larger for the coronal than the previous axial prescriptions, whether using foam or custom head restraint. Recall that the coronal acquisitions used L-R phase encoding and so perturbations of B0 change the distortion in that dimension to produce shearing. This clearly violates the rigid body assumption of the realignment algorithm and I can only assume that we are seeing some consequence of this reflected in the motion parameters. A good issue for someone with a lot of image processing expertise to dig into, or comment on. For the time being I am going with the hypothesis that the larger fluctuations for coronal than axial slices when using the custom restraint are due primarily to a greater sensitivity to B0 perturbation by chest movements when using L-R phase encoding in coronal slices. But I am leaving open the possibility of uncorrected direct motion.

The coronal data acquired with product EPI don't show the same systematic effects in pitch and yaw as the SMS data. Instead the traces are rather messy:

Product EPI, coronal slices. Left: foam restraint. Right: custom 3D printed headcase restraint

Is the absence of any dominant directionality in the traces a consequence of the reduced coverage in the product EPI scans? For now I'm assuming this is so. More on this in the next post.


Finally we can consider the sagittal scans. As a reminder, the slice direction is orthogonal between sagittal and axial slices, but they share a common phase encoding direction (anterior-posterior, or magnet Y axis). Differences between axial and sagittal data should thus reflect primarily differences in the slice dimension sensitivity to head motion and B0 modulation. Here are the motion parameters for the MB=6 sagittal scans with standard foam head restraint (left) versus the custom printed restraint (right):

MB=6, sagittal slices. Left: foam restraint. Right: custom 3D printed headcase restraint

When using custom head restraint the high frequency oscillations that were seen in the MB=6 axial scans are very similar to the oscillations in the MB=6 sagittal data, again consistent with B0 modulation from chest movements and implying a primary sensitivity in the phase encoding direction. What about other features that may differ between axial and sagittal data? There is a suggestion of reduced low frequency, drift-like motion for the sagittal scans. Until I've repeated the experiment I'd have to concede that gradient heating is the most likely explanation. Still, I wouldn't exclude the possibility just yet that perhaps the sagittal prescription has a lower sensitivity to both motion and B0 modulation from respiration, given that for axial scans we are slicing along the main magnetic field (Z) axis. It's something I plan on investigating.

The eleven sagittal slices acquired with product EPI have greater anatomical content than either the axial or coronal counterparts because I positioned them right down the midline. While there may still be issues with limited coverage compared to the full brain coverage permitted with SMS-EPI, we might expect a greater similarity with the MB=6 acquisition. Here are the sagittal EPI data:

Product EPI, sagittal slices. Left: foam restraint. Right: custom 3D printed headcase restraint

To my eye there is more similarity between the motion traces produced for sagittal product EPI and MB=6 than there was for either axial or coronal. Again, with N=1 we can't be sure, but this is an interesting starting point for future investigations where total brain coverage might be an important variable in the protocol. And we can't forget that the shearing produced in inferior portions of the brain will violate the rigid body assumption, as for the coronal data.


Final thoughts

In spite of the single set of tests presented here, the most important findings as reported in the last post are confirmed in the motion traces. The custom head restraint makes a truly massive difference to overall motion sensitivity. But the use of SMS-EPI does not ipso facto enhance the motion sensitivity. For matched spatial and temporal resolution we see just as much motion sensitivity for conventional EPI. Having reduced the head motion there is the residual issue of fluctuations at respiratory frequencies, caused by main field modulation. The sensitivity to both direct motion and respiratory effects varies considerably with assignment of the logical axes. No surprises there.

These results offered a few interesting new thoughts to guide future tests. How much does the total brain coverage affect realignment algorithm efficacy? When distortion effects clearly violate the rigid body assumption, what are the consequences when the head moves or when respiratory effects produce shearing? These are questions for another day. For now, though, I contend that we have enough evidence to suggest that most if not all fMRI studies - especially those using high spatial resolution - need to be doing even better with their head restraint, and that if one is contemplating a high-resolution fMRI experiment then a deeper consideration of respiratory effects is also warranted.

Thanks again to Jo Etzel for stimulating the current investigation with her own observations, and for all her stellar work since.