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BigStroke Pipeline — what to run, in what order

The phenomenological multi-scale stroke→gait→rehabilitation pipeline. One script per phase; later phases consume the outputs of earlier ones. Run from the repo root with the project venv active (source .venv/bin/activate).

Start here: the entry point that generates the data everything else reads is tvb_healthy_vs_stroke.py (Phase 1). Run it first.

Run order

# Phase Script Produces Reads
1 Phase 1 — cortex model tvb_motor_cortex_phase1.py TVB cortical firing-rate series —
1 Phase 1 — entry point tvb_healthy_vs_stroke.py tvb_output/comparison/tvb_{healthy,stroke}_*.h5 (CST drives) —
2 Phase 2 — spinal CPG tvb_phase2_spinal_cpg.py tvb_output/phase2/ gait/force figure; canonical simulate() Phase 1 .h5
2B Phase 2B — stroke severity tvb_phase2b_stroke_severity.py tvb_output/phase2b/ flaccid-severity figure imports Phase 2
3 Phase 3 — rehabilitation tvb_phase3_rehabilitation.py tvb_output/phase3/ recovery figure imports Phase 2
4 Phase 4 A–C — BOLD/FC/NIBS tvb_phase4_bold_nibs.py tvb_output/phase4/ BOLD + FC + NIBS figures imports Phase 2
4D Phase 4D — protocol comparison tvb_phase4d_rehab_comparison.py tvb_output/phase4d_overlay/ unified A–F comparison imports Phase 2

The one simulator that matters

tvb_phase2_spinal_cpg.py::simulate() is the single canonical CPG + muscle model. Every downstream phase imports and calls it, so improvements made there (e.g. the Phase 2B motoneuron-recruitment / flaccid-stroke model, and the optional epidural-SCS drive) propagate everywhere automatically.

If you add a new rehabilitation experiment, call p2.simulate(...) — do not copy the integration loop into a new file. (That copy-paste forking is exactly what archive/ cleaned up.)

simulate() key options:

  • recruit=True — motoneuron-pool recruitment gain (flaccid below C_CRIT)
  • scs_amp_L/scs_freq_L, scs_amp_R/scs_freq_R — epidural SCS sinusoidal drive

Severity presets

tvb_phase2_spinal_cpg.py::STROKE_SEVERITY maps clinical severity → descending-drive scale: healthy / mild / moderate / severe / complete. mild reproduces the original Phase-1 TVB deficit (back-compatible); severe/complete cross the recruitment threshold into a flaccid limb.

Archived / superseded

Earlier Phase 4D drafts live in archive/ (see archive/README.md). They are frozen references, not part of the live pipeline.

The other track

bigstroke_mn5/ is the separate spiking-network (NEST) track aimed at MareNostrum 5 — independent of this phenomenological pipeline. See bigstroke_mn5/README.md.