Optimization for long_fastsurfer, one view only for skull stripping#659
Closed
dkuegler wants to merge 0 commit into
Closed
Optimization for long_fastsurfer, one view only for skull stripping#659dkuegler wants to merge 0 commit into
dkuegler wants to merge 0 commit into
Conversation
Member
Author
|
Step 1 accomplished |
dkuegler
force-pushed
the
feature/long-only-one-view
branch
from
852fdb4 to
da32765
Compare
dkuegler
force-pushed
the
feature/long-only-one-view
branch
from
da32765 to
bbcf003
Compare
dkuegler
force-pushed
the
feature/long-only-one-view
branch
from
bbcf003 to
abb2cfe
Compare
dkuegler
force-pushed
the
feature/long-only-one-view
branch
from
abb2cfe to
931607e
Compare
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
This PR optimizes fastsurfer so that the skull stripping needed for longitudinal registration only uses one fastsurfer view.
Currently, run_prediction cannot be configured to only run on one view. But if it could, long_prepare_template would likely only need one view to compute the brainmask. Maybe we can even deactivate aseg and asegdkt output to save up time and disk space. This would then speed up this initial step.
Step 1: Modify run_prediction so the user is able to "deselect" views that should not be included. Syntax (example)
--cfg_ax noneStep 2 (optional) Modify run_predicrion so the user is able to "deselect" certain outputs. Syntax: no
--aseg_namemeans no aseg, unsure about--asegdkt_segfilemaybe none.Step 3: Test how reliable different view predict the brainmask.
Step 4: implement the best view for
long_prepare_template.sh.Step 5: Test impact on longitudinal pipeline.