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

ENH: Detect 3D BOLD series, warn and return empty workflow #2461

Merged
merged 4 commits into from
Jul 20, 2021
Merged

ENH: Detect 3D BOLD series, warn and return empty workflow #2461

merged 4 commits into from
Jul 20, 2021

Conversation

effigies
Copy link
Member

Closes #1931.

oesteban
oesteban approved these changes Jul 19, 2021
View reviewed changes
Copy link
Member

@oesteban oesteban left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggesting to make this more strict and demand >5 timepoints.

fmriprep/workflows/bold/base.py Outdated Show resolved Hide resolved
fmriprep/workflows/bold/base.py Outdated Show resolved Hide resolved
@effigies @oesteban
Apply suggestions from code review
c5227c1 
Co-authored-by: Oscar Esteban <code@oscaresteban.es>
@effigies
Copy link
Member Author

Sure.

@oesteban oesteban merged commit 98057c8 into nipreps:maint/20.2.x Jul 20, 2021
oesteban added a commit that referenced this pull request Jul 20, 2021
@oesteban
FIX: Address the problems of a sloppy merge
d44e9e6 
I precipitated the merge of #2461 without observing two issues:

- The bold workflow is provided with a list (not a str) with ME-EPI
- Test data (ds054) for CircleCI has only 5 timepoints, which triggered
  workflow skipping.

Both problems are addressed in this PR.

Continues: #2461.
@oesteban oesteban mentioned this pull request Jul 20, 2021
Merged
@oesteban oesteban linked an issue Jul 20, 2021 that may be closed by this pull request
Handle single-volume BOLD series #1931
Closed
@effigies effigies deleted the fix/detect_3d_bold branch July 20, 2021 15:22
@oesteban oesteban mentioned this pull request Aug 3, 2021
Merged
oesteban added a commit to oesteban/fmriprep that referenced this pull request Aug 4, 2021
@oesteban
FIX: Simplify STC logic for too short BOLD series
820dea4 
After nipreps#2461 and nipreps#2468, the ``TooShort`` value for running STC could not
be assigned.
This PR ignores manually set dummy timepoints, although the case when
this could be problematic is largely a very edge case (say you have only
7 timepoints and manually set 3 as dummy).

On the flip side, this PR drops the use of a function discontinued in
the latest niworkflows release, fixing a bug ahead of time.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@oesteban oesteban oesteban approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Handle single-volume BOLD series
2 participants
@effigies @oesteban