Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add motion parameter units to confounds sidecar #3231

Closed
tsalo opened this issue Feb 15, 2024 · 2 comments · Fixed by #3245
Closed

Add motion parameter units to confounds sidecar #3231

tsalo opened this issue Feb 15, 2024 · 2 comments · Fixed by #3245
Labels
feature
Milestone
24.0.0

Comments

@tsalo
Copy link
Collaborator

tsalo commented Feb 15, 2024 •
edited
Loading

What would you like to see added in fMRIPrep?

I think it would be nice if the confounds JSON file included the units of motion-related columns.

This could be done for all motion-related confounds, but I think it's most important for the rotation columns.

Do you have any interest in helping implement the feature?

Yes

Additional information / screenshots

This stems from PennLINC/xcp_d#1053. Basically, a user wants me to include metadata for the motion parameters in XCP-D. I'm happy to do that, but I thought it would make more sense to inherit the metadata from the preprocessing pipeline (i.e., fMRIPrep).
@tsalo tsalo added the feature label Feb 15, 2024
@tsalo
Copy link
Collaborator Author

tsalo commented Feb 23, 2024 •
edited
Loading

I know that the units of the motion parameters (mm for translations and radians for rotations) is enforced in BEP012 (Functional Derivatives) (see here) and the units are documented in the init_bold_confs_wf docstring, but neither location is particularly obvious to users.

@effigies effigies added this to the 24.0.0 milestone Feb 29, 2024
@effigies
Copy link
Member

I'm fine with this.

@tsalo tsalo mentioned this issue Mar 2, 2024
Merged
effigies added a commit that referenced this issue Mar 4, 2024
@tsalo @effigies
Add metadata for motion parameters (#3245)
ad65d0b 
Closes #3231.

## Changes proposed in this pull request

- Add metadata, including Units, for motion parameters (6 basic
parameters and FD).
- I included FD because it might be good to log the head radius that is
used to calculate it at some point (e.g., if
nipreps/nibabies#198 moves forward)

## Documentation that should be reviewed

none

---------

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
feature
Projects
None yet
Milestone
24.0.0
Development

Successfully merging a pull request may close this issue.

Add metadata for motion parameters tsalo/fmriprep
2 participants
@effigies @tsalo