Upsampling bold data in fmriprep

1

I just wanted to re-up the discussion on potential upsampling in fmriprep. The discussion came up before but got stuck somehow.

I see how upsampling can come with many caveats and therefore shouldn’t be a default, or maybe come with a warning to the users. On the other hand, it might improve spatial information in some cases without compromising data quality, e.g. here

In our special usecase, we’re trying to compare the effects of different preprocessing pipelines on the noise ceiling in our data. Generally we find that fmriprep delivers excellent results but we’d also like to try out upsampling. The new --output-spaces syntax in fmriprep looks like it might lend itself to accomodate resampling to different resolutions.

Could this be a potential feature that might be considered for future releases?

All the best
Oli

2

Looks like this is an open issue: FR: Arbitrary output resolution (for ``--output-spaces``) · Issue #1968 · nipreps/fmriprep · GitHub

The initial issue (Syntax for ``--output-spaces`` - specify (non)standard spaces · Issue #1604 · nipreps/fmriprep · GitHub) seemed to get positive response, so I think this is just going to be a matter of settling on a final syntax and then implementing it. Implementation should not be difficult, the main bottleneck is how much time people have.

3

Great to see! Thanks!