degibbs topup paired input image, no denoising - #50
Open
jwrenjarvis wants to merge 3 commits into
Open
Conversation
Author
|
added Ben as pull assignee option |
Collaborator
|
I think it looks fine. Just adjust for rpe images that do not have bval/bvec files. eg. designer_input_utils.py:313 |
jchen33344
approved these changes
Sep 9, 2025
Collaborator
|
I think it just doesn't pass the e2e test |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
When reverse phase encoding is added along with the degibbs flag, the b0_pair_topup.nii image is ran through an adjusted version of the degibbs wrapper. The degibbs wrapper can now take in 3D images and will take in other files instead of just the dwi.mif image. It will save out a .mif file to a new image called _rpg.mif and .nii image. If the input is b0_pair_topup.nii then it will not need to be a mif file and will not save out the bvec and bval. With degibbs and reversed phase encoding it will use the b0_pair_topup_rpg.nii file in topup. No other processing is done on the b0_pair_topup.nii image.