Upload folder using huggingface_hub

.gitattributes

@@ -60,3 +60,4 @@ saved_model/**/* 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
+cactus-axons/single-bundle-g070-icvf061.rpk filter=lfs diff=lfs merge=lfs -text

README.md

@@ -22,7 +22,7 @@ S = pack.replay(waveform, relaxation=True)
 
 | Substrate | Replay tiers | Size | License |
 |---|---|---|---|
-| [`cactus-axons/single-bundle-g070-icvf061-3T`](cactus-axons/single-bundle-g070-icvf061-3T.md) | C0 C1 C2 C3 C4 | 46.65 MB | CC-BY-4.0 |
+| [`cactus-axons/single-bundle-g070-icvf061`](cactus-axons/single-bundle-g070-icvf061.md) | C0 C1 C2 C3 C4 | 7.23 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

@@ -1,2 +1,2 @@
-5685ea727ea9ae67fa08055905c0c3de9202b7752a1514c2d854e248b4162adf  cactus-axons/single-bundle-g070-icvf061-3T.rpk
+d82fc41de0311c555c9f885e3d347f47bdacec0827e2e697b3901c107f0c4500  cactus-axons/single-bundle-g070-icvf061.rpk
 bb57348ea115be2900cfb44eb0ad13b3ba307f1d2b967086136d9fbd23423106  canonical-wm/g070-f055-3T.rpk

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

@@ -0,0 +1,122 @@
+{
+  "@context": {
+    "@vocab": "https://schema.org/",
+    "cr": "http://mlcommons.org/croissant/"
+  },
+  "@type": "Dataset",
+  "name": "cactus-axons/single-bundle-g070-icvf061",
+  "description": "dmipy-sim replay pack: compressed Monte-Carlo master walk (lowrank K=64) with replay envelope {'gradient': True, 'bulk_relaxation': True, 'surface_relaxivity': True, 'field': True, 'magnetization_transfer': True, '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",
+      "C3-field",
+      "C4-mt-two-pool-qMT"
+    ],
+    "c3_field": "3D myelin susceptibility field basis sampled along the walk (13-ch); any B0/orientation/chi",
+    "c4_mt": "geometry-derived two-pool qMT (f_b, k_f from myelin S/V); per-walker EMERGENT MT (binding coupled to diffusion) needs the intractable R/25 mesh walk",
+    "image": "single-bundle-g070-icvf061_xsection.png",
+    "field_strength_note": "B0 is a replay knob; pack is field-agnostic (id intentionally carries no field)"
+  },
+  "cr:replayEnvelope": {
+    "gradient": true,
+    "bulk_relaxation": true,
+    "surface_relaxivity": true,
+    "field": true,
+    "magnetization_transfer": true,
+    "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": 0.00246580676329679,
+    "floor_max": 0.01381479186198168,
+    "noise_floor": 0.007071067811865475,
+    "within_2x_floor": true,
+    "per_family": {
+      "OGSE1": {
+        "err_max": 5.2823911831579506e-05,
+        "floor_max": 0.011853765800666903
+      },
+      "OGSE2": {
+        "err_max": 4.542523613621486e-05,
+        "floor_max": 0.007125620416962809
+      },
+      "OGSE3": {
+        "err_max": 0.00017216395972078792,
+        "floor_max": 0.013183539653365321
+      },
+      "OGSE5": {
+        "err_max": 0.00246580676329679,
+        "floor_max": 0.009112497233388646
+      },
+      "PGSE": {
+        "err_max": 8.017915658644107e-05,
+        "floor_max": 0.007313176619329261
+      },
+      "SHORTD": {
+        "err_max": 0.00110073216164879,
+        "floor_max": 0.01381479186198168
+      }
+    },
+    "target_floor": 0.005,
+    "meets_target": false
+  },
+  "distribution": [
+    {
+      "@type": "cr:FileObject",
+      "name": "cactus-axons/single-bundle-g070-icvf061.rpk",
+      "encodingFormat": "application/octet-stream",
+      "contentUrl": null
+    }
+  ]
+}

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

@@ -0,0 +1,157 @@
+---
+license: cc-by-4.0
+tags:
+  - diffusion-mri
+  - monte-carlo
+  - replay-pack
+  - microstructure
+  - dmipy
+  - cactus
+  - white-matter
+pretty_name: single-bundle-g070-icvf061
+---
+
+# Substrate card — `cactus-axons/single-bundle-g070-icvf061`
+
+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).
+
+![single-bundle-g070-icvf061 cross-section](single-bundle-g070-icvf061_xsection.png)
+*Substrate cross-section: intra-axonal (blue), myelin (orange), extra-axonal (pale).*
+
+> **Field strength / acquisition are replay knobs, not baked in.** This pack replays **any** B0, gradient waveform, orientation, susceptibility, relaxation and (if present) surface/MT setting — so it is not specific to any scanner field.
+
+## 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 | ✅ | susceptibility field basis (any B0, direction, χ_iso, χ_aniso) |
+| C4 | Magnetization transfer | ✅ | MT saturation (Z-spectrum / MTR) |
+
+> Diffusivity is fixed at walk time (a geometry property, not a replay knob).
+
+## Fidelity
+
+| Metric | Value |
+|---|---|
+| Max replay error | 0.002466 |
+| MC noise floor | 0.01381 |
+| Within 2× floor | True |
+| Target floor σ* | 0.005 |
+| Meets σ* | False |
+| Walkers | 20000 |
+| Saved time points | 81 |
+| T_max (s) | 0.04 |
+| Compression | lowrank (K=64) |
+
+## Magnetization transfer (two-pool qMT)
+
+Geometry-derived pool (from the myelin surface-to-free-volume ratio); replay the Z-spectrum / MTR as a pool-level knob.
+
+| Parameter | Value |
+|---|---|
+| Bound fraction f_b | 0.08115 |
+| Forward rate k_f (1/s) | 88.32 |
+| Surface-to-volume (1/m) | 4.416e+06 |
+| T2 bound (s) | 1e-05 |
+
+## Load & replay
+
+```python
+import numpy as np
+from dmipy_sim import bank
+
+pack = bank.pull("cactus-axons/single-bundle-g070-icvf061", repo_id="dmrai-lab/substrate-bank")  # cached + hash-verified
+
+# C0/C1/C2 — build any waveform G on the pack's time grid (n_meas, pack.n_t, 3),
+# e.g. PGSE perpendicular vs parallel to the fibre axis (recovers the anisotropy):
+S = pack.replay(waveform, relaxation=True)          # C1; add rho=... for C2 surface
+# C1 knob — sweep per-compartment [T2, T1] (index = compartment id: 0 extra, 1 intra, 2 myelin):
+S = pack.replay(waveform, relaxation=True, T2=[0.06, 0.05, 0.010], T1=[1.0, 1.2, 0.44])
+# C3 field — any B0 / direction / susceptibility, off the stored field basis:
+S = pack.replay(waveform, B0=7.0, chi_aniso=-1e-7, b0_dir=[0,0,1], susc_refocus=False)
+# C4 MT — geometry-derived two-pool Z-spectrum / MTR:
+Z = pack.mt_zspectrum(np.linspace(-3e4, 3e4, 41), w1_hz=200.0, t_sat=0.5)
+mtr = pack.mtr(offset_hz=1e4, w1_hz=200.0, t_sat=0.5)
+```
+
+## 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.rpk

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d82fc41de0311c555c9f885e3d347f47bdacec0827e2e697b3901c107f0c4500
+size 7225430

cactus-axons/single-bundle-g070-icvf061__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
+
+

manifest.json

@@ -3,10 +3,10 @@
   "n_entries": 2,
   "entries": [
     {
-      "id": "cactus-axons/single-bundle-g070-icvf061-3T",
-      "file": "cactus-axons/single-bundle-g070-icvf061-3T.rpk",
-      "sha256": "5685ea727ea9ae67fa08055905c0c3de9202b7752a1514c2d854e248b4162adf",
-      "bytes": 46648180,
+      "id": "cactus-axons/single-bundle-g070-icvf061",
+      "file": "cactus-axons/single-bundle-g070-icvf061.rpk",
+      "sha256": "d82fc41de0311c555c9f885e3d347f47bdacec0827e2e697b3901c107f0c4500",
+      "bytes": 7225430,
       "license": "CC-BY-4.0",
       "replay_envelope": {
         "gradient": true,
@@ -48,6 +48,11 @@
             "n_t": 81,
             "scale": 3.629922866821289e-05,
             "nlevels": 127
+          },
+          "susc_basis": {
+            "K": 64,
+            "C": 13,
+            "T": 81
           }
         }
       }