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@@ -58,3 +58,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+cactus-axons/single-bundle-g070-icvf061-3T.rpk filter=lfs diff=lfs merge=lfs -text
+canonical-wm/g070-f055-3T.rpk filter=lfs diff=lfs merge=lfs -text

README.md

@@ -1,3 +1,28 @@
 ---
 license: cc-by-4.0
+tags:
+  - diffusion-mri
+  - monte-carlo
+  - replay-pack
+  - microstructure
+pretty_name: dmrai-lab substrate bank
 ---
+
+# dmrai-lab substrate bank
+
+Compressed Monte-Carlo **replay packs** (`.rpk`) for diffusion-MRI microstructure. Each pack is one master walk on a substrate plus the physics channels needed to **replay** any acquisition inside its certified envelope — *one walk, every acquisition* — in the open [Replay Pack Specification](https://github.com/dmrai-lab/replay-pack-spec) format.
+
+```python
+from dmipy_sim import bank
+pack = bank.pull("<id>", repo_id="dmrai-lab/substrate-bank")
+S = pack.replay(waveform, relaxation=True)
+```
+
+## Substrates
+
+| Substrate | Replay tiers | Size | License |
+|---|---|---|---|
+| [`cactus-axons/single-bundle-g070-icvf061-3T`](cactus-axons/single-bundle-g070-icvf061-3T.md) | C0 C1 C2 | 5.84 MB | CC-BY-4.0 |
+| [`canonical-wm/g070-f055-3T`](canonical-wm/g070-f055-3T.md) | C0 | 18.23 MB | CC-BY-4.0 |
+
+Each substrate links to its own **substrate card** with geometry, provenance, fidelity and load/replay instructions. Tier legend: C0 gradient · C1 bulk relaxation · C2 surface relaxivity · C3 field · C4 magnetization transfer.

SHA256SUMS

@@ -0,0 +1,2 @@
+9a7dd9015b0a5cf5a4e0715c406c483404e7a10234572a76f0504d1142ada5d3  cactus-axons/single-bundle-g070-icvf061-3T.rpk
+bb57348ea115be2900cfb44eb0ad13b3ba307f1d2b967086136d9fbd23423106  canonical-wm/g070-f055-3T.rpk

cactus-axons/single-bundle-g070-icvf061-3T.croissant.jsonld

@@ -0,0 +1,120 @@
+{
+  "@context": {
+    "@vocab": "https://schema.org/",
+    "cr": "http://mlcommons.org/croissant/"
+  },
+  "@type": "Dataset",
+  "name": "cactus-axons/single-bundle-g070-icvf061-3T",
+  "description": "dmipy-sim replay pack: compressed Monte-Carlo master walk (lowrank K=96) with replay envelope {'gradient': True, 'bulk_relaxation': True, 'surface_relaxivity': True, 'field': False, 'magnetization_transfer': False, 'diffusivity_fixed': True, 'acquisition': {'b_max': 3000000000.0, 'ogse_periods': [1, 2, 3, 5], 'B0_list': [3.0, 7.0, 11.7], 'note': 'temporal band set by max OGSE period / min delta'}}.",
+  "license": "CC-BY-4.0",
+  "citeAs": "Fick RHJ, dmrai-lab (2026). CACTUS single-bundle Monte-Carlo master walk. Geometry generator: Villarreal-Haro et al., CACTUS (https://github.com/Juanitovh/CACTUS).",
+  "cr:provenance": {
+    "substrate": "CACTUS single bundle",
+    "real_or_synthetic": "synthetic",
+    "generator": {
+      "name": "CACTUS",
+      "authors": "Villarreal-Haro et al.",
+      "url": "https://github.com/Juanitovh/CACTUS",
+      "patch": "workers/meta_grid.py: np.random.randn(n,3)->standard_normal((int(n),3)) for numba compat"
+    },
+    "g_ratio": 0.7,
+    "icvf": 0.6076,
+    "f_intra": 0.3486,
+    "f_myelin": 0.2589,
+    "f_extra": 0.3924,
+    "n_fibres": 366,
+    "box_um": [
+      30.0,
+      30.0,
+      30.0
+    ],
+    "fibre_axis": "x",
+    "TE": 0.04,
+    "feature_radius_um": {
+      "intra": 0.25,
+      "extra": 0.4
+    },
+    "boundary": "reflecting voxel box (extra pool)",
+    "cactus_config": "#Step1: Substrate Initialization parameters\n\n#### Algorithm parameters\noutfile cactus_bundle\nn_cores 10\nverbose 1 \n\n\n\n#substrate constant parameters\nn_bundles 1\nlenght_side 30\nmin_rad .27\nmax_rad 2.2\nbias -.03\n\n\n### combinational parameters\nnumber_of_repetitions 1\nicvf 0.65\ndispersion 10 \n\ngamma_theta 2.40 \ngamma_kappa 0.25 \n\n\n\n\n#Step 2: joint fibre optimization parameters \n\noptimization_tolerance 50\nmax_iterations 1500\nalpha 1\nsubdivisions_number 10\n\n\n#Step 3: Fibre radial growth (FRG) and meshing parameteres\n\ngrid_size 0.35\ngrowth_iterations 4\nn_segments 4\ncolorless 1\nsim_vol simulations\ninn_out outer\ng_ratio 0.7\nn_erode 0\n\n\n",
+    "optimized_final_header": [
+      "30",
+      "366",
+      "18"
+    ],
+    "tiers_present": [
+      "C0-gradient",
+      "C1-bulk-relaxation",
+      "C2-surface-relaxivity"
+    ],
+    "tiers_deferred": {
+      "C3_field": "rpk susceptibility channel is 2D translationally-invariant; CACTUS needs 3D field maps",
+      "C4_mt": "MT binding needs R/25 sub-step -> ~3.5M mesh reflections/walker on sub-micron features"
+    }
+  },
+  "cr:replayEnvelope": {
+    "gradient": true,
+    "bulk_relaxation": true,
+    "surface_relaxivity": true,
+    "field": false,
+    "magnetization_transfer": false,
+    "diffusivity_fixed": true,
+    "acquisition": {
+      "b_max": 3000000000.0,
+      "ogse_periods": [
+        1,
+        2,
+        3,
+        5
+      ],
+      "B0_list": [
+        3.0,
+        7.0,
+        11.7
+      ],
+      "note": "temporal band set by max OGSE period / min delta"
+    }
+  },
+  "cr:fidelity": {
+    "metric": "max_abs_complex_signal_error",
+    "err_max": 0.0005992180903185556,
+    "floor_max": 0.015136345027932882,
+    "noise_floor": 0.007071067811865475,
+    "within_2x_floor": true,
+    "per_family": {
+      "OGSE1": {
+        "err_max": 4.110324120514571e-05,
+        "floor_max": 0.01101313849143775
+      },
+      "OGSE2": {
+        "err_max": 3.0114713312470272e-05,
+        "floor_max": 0.007819370051004686
+      },
+      "OGSE3": {
+        "err_max": 0.00021818730268882545,
+        "floor_max": 0.008300622238353213
+      },
+      "OGSE5": {
+        "err_max": 0.00032166529279630717,
+        "floor_max": 0.008387572597074308
+      },
+      "PGSE": {
+        "err_max": 5.3429294722594866e-05,
+        "floor_max": 0.008324886028105324
+      },
+      "SHORTD": {
+        "err_max": 0.0005992180903185556,
+        "floor_max": 0.015136345027932882
+      }
+    },
+    "target_floor": 0.001,
+    "meets_target": false
+  },
+  "distribution": [
+    {
+      "@type": "cr:FileObject",
+      "name": "cactus-axons/single-bundle-g070-icvf061-3T.rpk",
+      "encodingFormat": "application/octet-stream",
+      "contentUrl": null
+    }
+  ]
+}

cactus-axons/single-bundle-g070-icvf061-3T.md

@@ -0,0 +1,140 @@
+---
+license: cc-by-4.0
+tags:
+  - diffusion-mri
+  - monte-carlo
+  - replay-pack
+  - microstructure
+  - dmipy
+  - cactus
+  - white-matter
+pretty_name: single-bundle-g070-icvf061-3T
+---
+
+# Substrate card — `cactus-axons/single-bundle-g070-icvf061-3T`
+
+A **replay pack** (`.rpk`) — a compressed Monte-Carlo master walk on a *synthetic* diffusion-MRI substrate, plus every physics channel needed to **replay** any acquisition inside its certified envelope without re-simulating. One walk, every acquisition. Format: the open [Replay Pack Specification](https://github.com/dmrai-lab/replay-pack-spec).
+
+## Geometry & provenance
+
+| Property | Value |
+|---|---|
+| Generator | [CACTUS](https://github.com/Juanitovh/CACTUS) |
+| Generator authors | Villarreal-Haro et al. |
+| Substrate | CACTUS single bundle |
+| Fibres | 366 |
+| g-ratio | 0.7 |
+| ICVF (intra+myelin) | 0.6076 |
+| f_intra | 0.3486 |
+| f_myelin | 0.2589 |
+| f_extra | 0.3924 |
+| Voxel box (µm) | [30.0, 30.0, 30.0] |
+| Fibre axis | x |
+| Boundary condition | reflecting voxel box (extra pool) |
+
+## Replay capability
+
+| Tier | Channel | Present | Meaning |
+|---|---|:--:|---|
+| C0 | Gradient | ✅ | positions — any q/b, direction, waveform (PGSE/PGSTE/OGSE/…) |
+| C1 | Bulk relaxation | ✅ | per-compartment T2/T1 via the compartment map |
+| C2 | Surface relaxivity | ✅ | boundary-local-time channel (any ρ) |
+| C3 | Field / susceptibility | — | stored susceptibility field maps (any B0, χ, orientation) |
+| C4 | Magnetization transfer | — | bound-fraction channel (MT/ihMT) |
+
+**Deferred tiers (with reason):**
+
+- **C3_field** — rpk susceptibility channel is 2D translationally-invariant; CACTUS needs 3D field maps
+- **C4_mt** — MT binding needs R/25 sub-step -> ~3.5M mesh reflections/walker on sub-micron features
+
+> Diffusivity is fixed at walk time (a geometry property, not a replay knob).
+
+## Fidelity
+
+| Metric | Value |
+|---|---|
+| Max replay error | 0.0005992 |
+| MC noise floor | 0.01514 |
+| Within 2× floor | True |
+| Target floor σ* | 0.001 |
+| Meets σ* | False |
+| Walkers | 20000 |
+| Saved time points | 81 |
+| T_max (s) | 0.04 |
+| Compression | lowrank (K=96) |
+
+## Load & replay
+
+```python
+import numpy as np
+from dmipy_sim import bank
+
+pack = bank.pull("cactus-axons/single-bundle-g070-icvf061-3T", repo_id="dmrai-lab/substrate-bank")  # cached + hash-verified
+
+# Build any waveform G on the pack's own time grid (shape (n_meas, pack.n_t, 3), T/m),
+# e.g. a PGSE perpendicular to the fibre axis, then replay it:
+S = pack.replay(waveform, relaxation=True)   # C1 relaxation; add rho=... for C2 surface
+# perpendicular vs parallel gradients recover the fibre anisotropy (S_perp > S_par).
+```
+
+## Generator configuration
+
+The exact generator config that produced this geometry (also embedded in the `.rpk` provenance):
+
+```
+#Step1: Substrate Initialization parameters
+
+#### Algorithm parameters
+outfile cactus_bundle
+n_cores 10
+verbose 1 
+
+
+
+#substrate constant parameters
+n_bundles 1
+lenght_side 30
+min_rad .27
+max_rad 2.2
+bias -.03
+
+
+### combinational parameters
+number_of_repetitions 1
+icvf 0.65
+dispersion 10 
+
+gamma_theta 2.40 
+gamma_kappa 0.25 
+
+
+
+
+#Step 2: joint fibre optimization parameters 
+
+optimization_tolerance 50
+max_iterations 1500
+alpha 1
+subdivisions_number 10
+
+
+#Step 3: Fibre radial growth (FRG) and meshing parameteres
+
+grid_size 0.35
+growth_iterations 4
+n_segments 4
+colorless 1
+sim_vol simulations
+inn_out outer
+g_ratio 0.7
+n_erode 0
+```
+
+Geometry header (`optimized_final.txt`): voxel_side=30, n_fibres=366, n_control_points=18.
+
+> Reproducibility note: workers/meta_grid.py: np.random.randn(n,3)->standard_normal((int(n),3)) for numba compat
+
+## Citation & license
+
+**License:** CC-BY-4.0  
+**Cite:** Fick RHJ, dmrai-lab (2026). CACTUS single-bundle Monte-Carlo master walk. Geometry generator: Villarreal-Haro et al., CACTUS (https://github.com/Juanitovh/CACTUS).

cactus-axons/single-bundle-g070-icvf061-3T.rpk

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+version https://git-lfs.github.com/spec/v1
+oid sha256:9a7dd9015b0a5cf5a4e0715c406c483404e7a10234572a76f0504d1142ada5d3
+size 5838772

cactus-axons/single-bundle-g070-icvf061-3T__cactus_config.txt

@@ -0,0 +1,48 @@
+#Step1: Substrate Initialization parameters
+
+#### Algorithm parameters
+outfile cactus_bundle
+n_cores 10
+verbose 1 
+
+
+
+#substrate constant parameters
+n_bundles 1
+lenght_side 30
+min_rad .27
+max_rad 2.2
+bias -.03
+
+
+### combinational parameters
+number_of_repetitions 1
+icvf 0.65
+dispersion 10 
+
+gamma_theta 2.40 
+gamma_kappa 0.25 
+
+
+
+
+#Step 2: joint fibre optimization parameters 
+
+optimization_tolerance 50
+max_iterations 1500
+alpha 1
+subdivisions_number 10
+
+
+#Step 3: Fibre radial growth (FRG) and meshing parameteres
+
+grid_size 0.35
+growth_iterations 4
+n_segments 4
+colorless 1
+sim_vol simulations
+inn_out outer
+g_ratio 0.7
+n_erode 0
+
+

canonical-wm/g070-f055-3T.croissant.jsonld

@@ -0,0 +1,83 @@
+{
+  "@context": {
+    "@vocab": "https://schema.org/",
+    "cr": "http://mlcommons.org/croissant/"
+  },
+  "@type": "Dataset",
+  "name": "canonical-wm/g070-f055-3T",
+  "description": "dmipy-sim replay pack: compressed Monte-Carlo master walk (lowrank K=64) with replay envelope {'gradient': True, 'rf': True, 'B0_any': True, 'orientation_any': True, 'T1T2': True, 'rho': False, 'mt': False, 'permeability': False, 'diffusivity_fixed': True, 'acquisition': {'b_max': 3000000000.0, 'ogse_periods': [1, 2, 3, 5], 'B0_list': [3.0, 7.0, 11.7], 'note': 'temporal band set by max OGSE period / min delta'}}.",
+  "license": "CC-BY-4.0",
+  "citeAs": "Fick RHJ, dmrai-lab (2026), canonical WM master (synthetic).",
+  "cr:provenance": {
+    "g_ratio": 0.7,
+    "packing_density": 0.55,
+    "real_or_synthetic": "synthetic"
+  },
+  "cr:replayEnvelope": {
+    "gradient": true,
+    "rf": true,
+    "B0_any": true,
+    "orientation_any": true,
+    "T1T2": true,
+    "rho": false,
+    "mt": false,
+    "permeability": false,
+    "diffusivity_fixed": true,
+    "acquisition": {
+      "b_max": 3000000000.0,
+      "ogse_periods": [
+        1,
+        2,
+        3,
+        5
+      ],
+      "B0_list": [
+        3.0,
+        7.0,
+        11.7
+      ],
+      "note": "temporal band set by max OGSE period / min delta"
+    }
+  },
+  "cr:fidelity": {
+    "metric": "max_abs_complex_signal_error",
+    "err_max": 0.0015449349215161125,
+    "floor_max": 0.007417712466507749,
+    "noise_floor": 0.002886751345948129,
+    "within_2x_floor": true,
+    "per_family": {
+      "OGSE1": {
+        "err_max": 2.6567877097349795e-05,
+        "floor_max": 0.007417712466507749
+      },
+      "OGSE2": {
+        "err_max": 5.227884402603549e-05,
+        "floor_max": 0.004460657597099843
+      },
+      "OGSE3": {
+        "err_max": 0.0002155028703048945,
+        "floor_max": 0.005062851187307158
+      },
+      "OGSE5": {
+        "err_max": 0.00032346565433251715,
+        "floor_max": 0.0037408410155284743
+      },
+      "PGSE": {
+        "err_max": 4.928880879743661e-05,
+        "floor_max": 0.004254416190880235
+      },
+      "SHORTD": {
+        "err_max": 0.0015449349215161125,
+        "floor_max": 0.003591027423547303
+      }
+    }
+  },
+  "distribution": [
+    {
+      "@type": "cr:FileObject",
+      "name": "canonical-wm/g070-f055-3T.rpk",
+      "encodingFormat": "application/octet-stream",
+      "contentUrl": null
+    }
+  ]
+}

canonical-wm/g070-f055-3T.md

@@ -0,0 +1,64 @@
+---
+license: cc-by-4.0
+tags:
+  - diffusion-mri
+  - monte-carlo
+  - replay-pack
+  - microstructure
+  - dmipy
+  - white-matter
+pretty_name: g070-f055-3T
+---
+
+# Substrate card — `canonical-wm/g070-f055-3T`
+
+A **replay pack** (`.rpk`) — a compressed Monte-Carlo master walk on a *synthetic* diffusion-MRI substrate, plus every physics channel needed to **replay** any acquisition inside its certified envelope without re-simulating. One walk, every acquisition. Format: the open [Replay Pack Specification](https://github.com/dmrai-lab/replay-pack-spec).
+
+## Geometry & provenance
+
+| Property | Value |
+|---|---|
+| g-ratio | 0.7 |
+
+## Replay capability
+
+| Tier | Channel | Present | Meaning |
+|---|---|:--:|---|
+| C0 | Gradient | ✅ | positions — any q/b, direction, waveform (PGSE/PGSTE/OGSE/…) |
+| C1 | Bulk relaxation | — | per-compartment T2/T1 via the compartment map |
+| C2 | Surface relaxivity | — | boundary-local-time channel (any ρ) |
+| C3 | Field / susceptibility | — | stored susceptibility field maps (any B0, χ, orientation) |
+| C4 | Magnetization transfer | — | bound-fraction channel (MT/ihMT) |
+
+> Diffusivity is fixed at walk time (a geometry property, not a replay knob).
+
+## Fidelity
+
+| Metric | Value |
+|---|---|
+| Max replay error | 0.001545 |
+| MC noise floor | 0.007418 |
+| Within 2× floor | True |
+| Walkers | 120000 |
+| Saved time points | 301 |
+| T_max (s) | 0.06 |
+| Compression | lowrank (K=64) |
+
+## Load & replay
+
+```python
+import numpy as np
+from dmipy_sim import bank
+
+pack = bank.pull("canonical-wm/g070-f055-3T", repo_id="dmrai-lab/substrate-bank")  # cached + hash-verified
+
+# Build any waveform G on the pack's own time grid (shape (n_meas, pack.n_t, 3), T/m),
+# e.g. a PGSE perpendicular to the fibre axis, then replay it:
+S = pack.replay(waveform, relaxation=True)   # C1 relaxation; add rho=... for C2 surface
+# perpendicular vs parallel gradients recover the fibre anisotropy (S_perp > S_par).
+```
+
+## Citation & license
+
+**License:** CC-BY-4.0  
+**Cite:** Fick RHJ, dmrai-lab (2026), canonical WM master (synthetic).

canonical-wm/g070-f055-3T.rpk

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+size 18231174

manifest.json

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+{
+  "schema": "dmipy-sim substrate-bank/1.1",
+  "n_entries": 2,
+  "entries": [
+    {
+      "id": "cactus-axons/single-bundle-g070-icvf061-3T",
+      "file": "cactus-axons/single-bundle-g070-icvf061-3T.rpk",
+      "sha256": "9a7dd9015b0a5cf5a4e0715c406c483404e7a10234572a76f0504d1142ada5d3",
+      "bytes": 5838772,
+      "license": "CC-BY-4.0",
+      "replay_envelope": {
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+        "bulk_relaxation": true,
+        "surface_relaxivity": true,
+        "field": false,
+        "magnetization_transfer": false,
+        "diffusivity_fixed": true,
+        "acquisition": {
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+          "note": "temporal band set by max OGSE period / min delta"
+        }
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+      "compression": {
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+        "K": 96,
+        "walker_preserving": true,
+        "channels": {
+          "compartment": {
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+            "fractional": false,
+            "n_t": 81
+          },
+          "boundary_local_time": {
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+            "mode": "dense",
+            "n_t": 81,
+            "scale": 3.8564205169677734e-05,
+            "nlevels": 127
+          }
+        }
+      }
+    },
+    {
+      "id": "canonical-wm/g070-f055-3T",
+      "file": "canonical-wm/g070-f055-3T.rpk",
+      "sha256": "bb57348ea115be2900cfb44eb0ad13b3ba307f1d2b967086136d9fbd23423106",
+      "bytes": 18231174,
+      "license": "CC-BY-4.0",
+      "replay_envelope": {
+        "gradient": true,
+        "rf": true,
+        "B0_any": true,
+        "orientation_any": true,
+        "T1T2": true,
+        "rho": false,
+        "mt": false,
+        "permeability": false,
+        "diffusivity_fixed": true,
+        "acquisition": {
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+          "ogse_periods": [
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+            2,
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+            11.7
+          ],
+          "note": "temporal band set by max OGSE period / min delta"
+        }
+      },
+      "fidelity": 0.0015449349215161125,
+      "compression": {
+        "method": "lowrank",
+        "K": 64,
+        "walker_preserving": true
+      }
+    }
+  ]
+}