HT local subregions testing - #1
Open
htregidgo wants to merge 4 commits into
Open
Conversation
htregidgo
commented
May 14, 2026
htregidgo
commented
Collaborator
- Add local subregions test config profiles
- Document subregions smoke-test outputs
Refactor the shared subregions smoke-test harness so Henry and Jackson can run it without editing hard-coded paths in the script. The script now looks for repo-relative JSON profile pairs and uses the first one whose required FreeSurfer, subject, segmentation, and DTI paths exist. Add Henry-specific DTI and multichannel JSON files while leaving Jackson's existing JSON files as the fallback profile. Keep temp and output locations separate for DTI, standard thalamus, and multichannel runs so results remain inspectable and avoid filename collisions. Replace the hard-coded means_groupings.json path in thalamusDTI.py with a path derived from the module location, so the support file is loaded from the repo on either machine.
Add notes to the local subregions test harness explaining the three objects it drives: the DTI-aware run, the standard thalamus run, and the multi-channel DTI/FA run. Annotate each process.py-style command group with the temp files or final outputs it writes. This keeps the dirty shared harness easier to inspect after long local smoke tests without changing runtime behavior.
jnolan14
marked this pull request as ready for review
May 27, 2026 14:22
Add shared Gaussian helpers for diagonal and full-covariance subregions fitting, including likelihoods, posterior parameter updates, covariance conversion for GEMS, and validation for covariance-mode inputs. Wire covariance_mode through MeshModel and ThalamicNucleiDTI while preserving diagonal mode as the default. Refactor image fitting and final posterior extraction to use the shared helpers, and pass full covariance matrices to GEMS in both covariance modes. Update DTI hyperparameter estimation so multi-channel runs produce channel-aware meanHyper arrays while keeping nHyper one-dimensional. Add focused pytest coverage for the helper math, covariance shape handling, low-mass fallbacks, singular covariance rejection, and the full mean-prior cost.
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.