Add support for running group-level command on connectivity matrices#948
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HippocampusGirl wants to merge 12 commits intomainfrom
Open
Add support for running group-level command on connectivity matrices#948HippocampusGirl wants to merge 12 commits intomainfrom
HippocampusGirl wants to merge 12 commits intomainfrom
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Pull request overview
This PR adds support for running the group-level command on connectivity (correlation/covariance) matrices by integrating matrix-aware BIDS naming/loading and converting correlation matrices into voxelwise-compatible effect/variance images.
Changes:
- Add matrix-aware BIDS derivatives mapping for
correlation_matrix/covariance_matrixand adjust grouping behavior. - Convert subject-level correlation matrices to Fisher z “effect” and corresponding “variance” images for group-level model fitting.
- Make masks optional throughout group-level fit/export paths and update handling of inconsistent export statistics.
Reviewed changes
Copilot reviewed 9 out of 9 changed files in this pull request and generated 9 comments.
Show a summary per file
| File | Description |
|---|---|
src/halfpipe/stats/fit.py |
Allows mask_files to be optional and updates mask/NaN handling during data loading. |
src/halfpipe/stats/base.py |
Modifies map-writing save behavior (but currently introduces a debugger breakpoint and changes save API). |
src/halfpipe/result/bids/images.py |
Adds explicit BIDS mapping for matrix outputs via suffix=matrix + desc=.... |
src/halfpipe/interfaces/result/make.py |
Removes composite-attribute expansion logic previously used to split keys like correlation_matrix. |
src/halfpipe/cli/commands/group_level/run.py |
Adds Fisher z transform step producing effect/variance NIfTIs from correlation matrices prior to aggregation/fitting. |
src/halfpipe/cli/commands/group_level/export.py |
Makes mask optional for export and changes how inconsistent statistics across subjects are handled. |
src/halfpipe/cli/commands/group_level/design.py |
Allows connectivity-matrix inputs to pass filtering (correlation_matrix added). |
src/halfpipe/cli/commands/group_level/between.py |
Treats masks as optional and avoids adding missing masks to metadata.sources. |
src/halfpipe/cli/commands/group_level/base.py |
Adds correlation_matrix -> effect alias in group-level image key normalization. |
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Pull request overview
Copilot reviewed 24 out of 24 changed files in this pull request and generated 9 comments.
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