fmriprep --minimal mode #2806
Assignees
Comments
|
Relates to #2207. |
|
@Lestropie I really hoped to be able to get to this during July, but failed. I'm now going to be out for three weeks for vacation and a dedicated sprint on another topic, so hope to be able to start to get back to this the week of Aug 22. Please do feel free to push on PRs or add notes of any roadblocks you're having or things you need input on. |
effigies
added a commit
that referenced
this issue
Feb 2, 2023
Back when I commenced some work on #2207 (from which I'll need to familiarise myself with #2913), I started by looking at the CLI and thinking about what the right interface would be for such a capability (see eg. #2805, #2806). I immediately found some command-line options that really felt as though they were in the wrong place. So here I've separated out the set of CLI changes that I'd generated in the course of that little experiment. The git diff is quite unclean, so I've produced the set of options that would be moved and their corresponding old and new option groups. | Option | Old option group | New option group | |-----------------------------|-------------------------------|------------------------------------------------------| | `--anat-only` | Options to handle performance | Options for performing only a subset of the workflow | | `--boilerplate-only` | Options to handle performance | Options for performing only a subset of the workflow | | `--md-only-boilerplate` | Options to handle performance | Options for modulating outputs | | `--cifti-output` | Surface preprocessing options | Workflow configuration | | `--error-on-aroma-warnings` | Options to handle performance | Specific options for running ICA_AROMA | | `--verbose` | Options to handle performance | Other options | | `--me-output-echos` | Workflow configuration | Options for modulating outputs | | `--medial-surface-nan` | Workflow configuration | Options for modulating outputs | | `--no-submm-recon` | Surface preprocessing options | Specific options for FreeSurfer processing | | `--output-layout` | Other options | Options for modulating outputs | | `--sloppy` | Other options | Options to handle performance | | `--track-carbon` | Other options | Options for carbon tracking | | `--country-code` | Other options | Options for carbon tracking | New option groups: - "Options for performing only a subset of the workflow" - "Options for modulating outputs" - "Options for carbon tracking" Deleted option groups: - "Surface preprocessing options" In particular, "Options for performing only a subset of the workflow" is what I was looking for in the context of #2207, where I had initially added command-line options "`--fmri_withhold`" and "`--fmri_regenerate`" (the naming of such options should perhaps be discussed in #2913). Open to modification of proposed changes, or indeed addition of other changes (since this would be a good opportunity to review placement of the complete set of command-line options). For instance I'm currently looking at `[ --output-spaces, --cifti-output, --me-output-echos ]` as a candidate option group.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
A version of fmriprep that produces a set of derivatives necessary to support fmriprep-apply and nothing else.
Minimally, this requires:
The text was updated successfully, but these errors were encountered: