Switch to using mean magnitude for output moco_params.tsv file used for QC
#4396
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The purpose of this QC file is to identify the amount of motion in each volume (that is, at each time point), so that motion-related fluctuation in the signal can be corrected for. Having the average of the signed X and Y values is not useful for this, because a lot of left-right motion (or front-back motion) could mostly cancel out, and look the same as not having much motion at all. This is potentially confusing, and prone to misuse. In contrast, the mean magnitude is only small when there is not much total motion, and it is scale-invariant with the number of Z slices.
mguaypaq
added
enhancement
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I fixed the description of the output files in the help message for |
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Ah, I forgot to update the tests. Sorry! |
I just used the current outputs, since we don't really have any principled values to compare with.
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Bug fixed, tests updated, ready for review again. |
joshuacwnewton
approved these changes
Mar 8, 2024
joshuacwnewton
changed the title
moco_params.tsv file used for QC
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((Updated the PR title, just because there also exists a "QC Report" for motion correction, and I was a little confused at first, hehe.)) |
Co-authored-by: Joshua Newton <joshuacwnewton@gmail.com>
mguaypaq
added a commit
that referenced
this pull request
Mar 13, 2024
The columns were changed in #4396, but the tutorial changes should only be merged when SCT v6.3 gets released, since the website updates immediately.
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The purpose of this QC file is to identify the amount of motion in each volume (that is, at each time point), so that motion-related fluctuation in the signal can be corrected for.
Having the average of the signed X and Y values is not useful for this, because a lot of left-right motion (or front-back motion) could mostly cancel out, and look the same as not having much motion at all. This is potentially confusing, and prone to misuse.
In contrast, the mean magnitude is only small when there is not much total motion, and it is scale-invariant with the number of Z slices.
Note: the formula for magnitude,$\sqrt{X^2+Y^2}$ , only makes sense when $X$ and $Y$ have the same units (that is, millimeters, not voxels). So, I considered whether we should also use the voxel dimensions in the calculation, and concluded that we shouldn't:
sct_fmri_mococommand from our tutorial to get a baseline filemoco_params.tsv.moco_params.tsvapproximately doubled. Which means that the coordinates are in physical units, not integer array coordinates.moco_params.tsvwere very different, basically unrelated. Which further confirms that ANTS registration takes into account physical units, I guess.Fixes #4344.