set rat-specific defaults for FD calculations

[eilidhmacnicol]

Currently, rotational FD components are calculated as the displacement on the surface of a sphere with a radius of 50 mm, because it:

is approximately the mean distance from the cerebral cortex to the center of the head
according to Power et al., 2012.

This is obviously not appropriate for rodents, so we would expect rat data to exaggerate the contribution of rotational movement in FD calculations.

The only adjustment (so far) is to adjust the default radius if the species is non-human. This is less trivial for rats than humans, since brains of the former are not spherical. In my experience, roll rotations are more likely to occur if the animal is fixed in place with ear and bite bars, so I set the radius to be half of the average lateral width for 90-day-old rats in Gefen et al. (2004; https://doi.org/10.1089/089771503770802853). This can still be adjusted by changing the defaults on the command line, but it would provide a better default with the --species rat flag for minimal user intervention.

I'll try re-running this on some data to see if the default 0.2mm FD is still reasonable in rats given these changes.
@oesteban do you have any insight on why this threshold was chosen? Are there any other parameters you can think of that I should check?

[pep8speaks]

Hello @eilidhmacnicol, Thank you for updating!

Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, pip install flake8 and then run flake8 niworkflows.

Comment last updated at 2022-08-16 08:34:02 UTC

[eilidhmacnicol]

Quick test with nipype's framewise displacement on the same.1D file from 3dVolreg:
With the default (radius = 50.0)
fd_power_default.pdf
Adjusted radius (radius = 7.5)
fd_power_7point5.pdf

Data not shown, radius = 5.0 and radius = 10.0. Not a lot of difference between them, so radius = 7.5 is also a nice mid point as well as being the most likely rotational orientation.

[eilidhmacnicol]

So after a quick review fd-radius is not set on the command line, meaning this should be the only change necessary.

However, for some reason the T1w tests aren't working. @oesteban do you have any clues why summary_bg_mad would be recorded as zero?

EDIT: It seems like the head masking failed (in that it produced a mask, but it was very small). Could this be an impact of fd-radius?

[oesteban]

Hi @eilidhmacnicol, can you rebase to upstream/master? I have fixed some issues making CI fail.

[eilidhmacnicol]

Success! Anything else @oesteban or will I merge?