not all MB4 fMRI scans are free of gradients and banding

I was encouraged by the images in the previous post: it looked like the gradient and banding ("washing out") artifacts were not visible in the MB4 people. I need to revise that a bit: I do have bands and gradients in at least some MB4 people, though to a much lesser degree than in our MB8 datasets. How much this affects our task analyses is still to be determined.

On the left is the same MB4 person and run from the previous post (27 September 2017), voxelwise standard deviation over time of a task fMRI run, after going through the HCP minimal preprocessing pipelines. I was glad to see that the vessels were brightest (as they should be), though concerned about the frontal dropout. The person on the right is another person scanned at MB4 (doing the same task; same encoding, scanner, etc.); same preprocessing and color scaling for both.

The vessels clearly don't stand out as much in the person on the right. It's hard to tell in the above image, but there's a gradient in the standard deviation and tSNR images, with better signal on the edges than in the center of the brain. Below is another run from the person on the right, tSNR calculated on the images ready to go into afni for GLM calculation (so through the HCP minimal preprocessing pipelines, plus smoothing and voxelwise normalizing). This tSNR image is shown at six different color scalings; it's easier to see interactively (download the NIfTI here), but hopefully it's clear that the darker colors (lower tSNR) spreads from the center of the brain to the edges, rather than uniformly.

Here is the same person and run again, with the standard deviation (first two) and tSNR (right pane) of the raw (no preprocessing, first and lower) and minimally preprocessed (right two) images. I marked a banding distortion with green lines, as well as the frontal dropout. The banding is perfectly horizontal in the raw image, at 1/4 of the way up the image (see larger image), which makes sense, since this is an MB4 acquisition. I included the larger view of this raw image since all three banding artifacts are somewhat visible; in our dataset the inferior band is generally the most prominent.

The banding and gradient artifacts are certainly less visually prominent in our MB4 than our MB8 images, but they are present in some MB4 people. I haven't systematically evaluated (and probably won't be able to soon) all of our participants, so don't have a sense of how often this occurs, or how much it impacts detection of task BOLD (which is of course the key question).

Below the jump: movement regressors for the two runs in the top image; the person with the banding and gradients had very low motion; less than the person from the September post.




Realignment parameters from the minimal preprocessing pipelines, plus FD and enorm, for the two runs shown in the top image. The left-hand person (from the September post) is first, marked with an "S"; the person on the right (and other images) is in the second plot. This new person had very little motion (or even apparent motion) in their runs.

  Vertical grey lines mark one-minute intervals (entire run about 13 minutes); horizontal green lines are task blocks.