Repository navigation
Curated head shape for FSAverage - #14462
Open
christianbrodbeck wants to merge 2 commits into
Open
christianbrodbeck wants to merge 2 commits into
christianbrodbeck wants to merge 2 commits into
Conversation
Both the coregistration GUI and plot_alignment looked for outer_skin.surf before the subject's own -head.fif, so a curated head surface (such as the fsaverage head packaged with MNE) was never used when a watershed outer skin was also present.
Both fsaverage zip files ship the watershed outer skin as bem/fsaverage-head.fif, so the smoother head surface packaged with MNE (previously only reachable through create_default_subject, which needs a FreeSurfer install) was never used. This modification copies it over the extracted file when fsaverage-head.fif was missing before the downloads; existing files are left alone, consistent with the no-overwrite rule.
christianbrodbeck
force-pushed
the
fsaverage
branch
from
October 27, 2026 17:14
c2cd91f to
80fea88
Compare
This branch has not been deployed
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
What does this implement/fix?
MNE-Python ships a curated head shape for FSAverage that I used to use for coregistration (left-most picture). With the
fetch_fsaveragefunction this head shape is not used anymore, and the result of watershed is used instead (middle). Was this change intentional? If not, this PR restores the old behavior by copying the curated head shape from mne-python infetch_fsaverage, and using it in the coregistration GUI.