Tim Coalson

Basically, that max is intended to only prevent zero divided by zero. If the VN doesn't match the data, there is probably a better solution, and it would be good...

wb_command and applywarp should both output 0 when asked to sample outside the FoV, so the output of OneStepResample should not have small values because of that. Do you know...

So, to clarify, you are running MIGP on data that has already been through tICA cleaning?

So, tICA is finding the dilated region (single subject? semi-common problem area in the study?), calling it artifact/nuisance, and effectively reverting it to the undilated data, but with rounding error....

For this one purpose we could hide the problem behind the zero-variance handling, sure, but that doesn't change the fact that the tICA cleaned output currently produces values that are...

The general solution is to compute an explicit mask of where we had to dilate zeros out of the data, and keep that alongside the timeseries. A less certain possibility...

Suggested fix added as https://github.com/Washington-University/HCPpipelines/commit/d73c7d9fe767de2c2441b3d5cb9baa966ed8eb31

Another post-hoc strategy would be to detect per-run locations where the vn file has excessively small values, and use that to do another round of dilation after tICA.

We didn't change the permissions in the existing release zip, but we did change it on the folders that get zipped to make them. It has been longer than expected...

`you have held broken packages` Some package you seem to have pinned is preventing the zlib headers from being a candidate for installation, you should unpin and fix broken packages...