More robust bvecs/bvals compatibility #2602
Open
Conversation
This file contains 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
Where the gradient direction vector is zero, but the b-value is non-zero, when FSL's "eddy" attempts to rotate the directions of b>0 volumes according to subject rotation, this results in corrupted gradient directions. This change prevents such data from reaching "eddy" within dwifslpreproc, by detecting volumes where the gradient vector is zero and the b-value is non-zero but is classified by MRtrix3 as non-zero based on BZeroThreshold and forcing the value within the bvals file to be zero. Relates to #2577.
|
@Lestropie generating a Singularity image for that branch to test today. |
|
That works. |
Lestropie
changed the title
|
Scope of PR has been expanded from just "clamp b-values interpreted by MRtrix3 as b=0 to a value of 0 when exporting bvals" to "change bvecs&bvals import/export for more robust interplay with FSL", closing #2577 in the process. The new tests (here attributed to |
Lestropie
added a commit
that referenced
this pull request
Feb 12, 2025
Lestropie
force-pushed
the
bval_clamp_zero
branch
from
6e90b23 to
ecaacef
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
Potential solution to #2577. Not a unique solution, but works for me, and the warning message is generated appropriately.
@araikes want to test?