First Full Refactor

Release 2026

I have been lazy in updating this repository, but got around to refactoring it into something more useable and testable. Refactoring was aided by Codex, partly to see how well it was able to take an existing fractured repository and build it into something that is less fractured. I would call it a success.

Updates

• Switched to configuration based scripts instead of full monolithic pipeline
• Improved modularity of code
• Built tests
• Added output for common neuroimaging package formats (AFNI, CONN, SPM, etc...)