Super-squash branch 'main' using huggingface_hub

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LICENSING.md

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+# Licensing
+
+The asset of this dataset is dual-licensed.
+
+## Research and non-profit use — CC BY-NC-SA 4.0
+
+The asset, its manifest and its checks are available under the
+[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License](https://creativecommons.org/licenses/by-nc-sa/4.0/).
+You may download, replay, redistribute and build upon them for research, teaching and any other non-commercial
+purpose, as long as you credit this dataset and its source geometry (the `citation` field of every pack) and
+release what you build upon them under the same terms.
+
+## Commercial use
+
+A commercial licence is available under separately negotiated terms for use that makes money: inside a product,
+a paid service, contract research, or the training of a model that is sold. It lifts the non-commercial and
+share-alike obligations.
+
+📧 **rutger.fick@dmrai-lab.org**
+
+## What the licence covers, and what it does not
+
+The licence covers the simulated records in the packs: the walkers' paths, occupancies, wall contacts and field
+samples, their coefficients, and the certificates. The **source geometry** each pack was simulated on keeps its
+own licence, recorded in the pack's `license` field and in the manifest, and this dataset never relicenses it.
+The replay-pack **format** is a separate, openly licensed specification (CC-BY-4.0 text, Apache-2.0 reference code):
+anyone may produce and read packs under their own terms.
+
+Copies of a pack obtained under an earlier licence of this dataset keep that licence; these terms apply from the
+revision that carries this file.

README.md

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+---
+license:
+  - cc-by-nc-sa-4.0
+  - other
+pretty_name: "MASiVar sub-cIs1 as a replay phantom: the MT-CSD FOD field, tissue fractions and an 84-region parcellation"
+tags:
+  - diffusion-mri
+  - replay
+  - phantom
+  - connectome
+---
+
+# MASiVar `sub-cIs1` as a compositional replay phantom
+
+The input of the brain Space (`rfick/brain-zero`, dmrai-lab/disco-space#8): one real scan reconstructed **once, offline,
+by dmipy-fit alone** into the arrays a compositional replay phantom composes with replay packs. Nothing here is a
+diffusion-weighted image: the subject's DWI is not redistributed (it is on OpenNeuro under CC0); this dataset is what
+multi-tissue CSD made of it, plus a parcellation of the subject's T1.
+
+## Source
+
+* Subject `sub-cIs1`, session `ses-s1Ax1`, the first scan, of **MASiVar** (OpenNeuro `ds003416`, version 2.0.2,
+  DOI 10.18112/openneuro.ds003416.v2.0.2; Cai et al., *MASiVar: Multisite, Multiscanner, and Multisubject
+  Acquisitions for Studying Variability in Diffusion Weighted MRI*, Magnetic Resonance in Medicine 2021,
+  DOI 10.1002/mrm.28926). Licence of the source: CC0.
+* The scan: 3 T, 2.5 mm isotropic, five shells b = 1000 / 1500 / 2000 / 2500 / 3000 s/mm² with 96 directions each and
+  one b = 0 per shell (485 measurements), taken from the dataset's PreQual v1.0.0 derivative (denoised, susceptibility-,
+  eddy- and motion-corrected), the five per-shell files merged. The sidecars record no echo time or pulse timing.
+* The T1: `ses-s1Ax2`, 1 mm.
+
+## What is in it
+
+| file | content |
+|---|---|
+| `manifest.json` | the subject, the source DOIs and licence, the grid (shape, voxel size, affine), the protocol (b-values, image-frame directions), the FOD basis, the reconstruction record (tool, commit, responses, solver), the parcellation record |
+| `fod_wm.npy` | `(X, Y, Z, 45)` float32: the white-matter FOD as real spherical harmonics to order 8 in the image frame, as dmipy-fit's CSD emits them (tournier07 ordering), 0 outside the mask |
+| `fractions.npy` | `(X, Y, Z, 3)` float16: the geometric WM / GM / CSF fractions of the multi-tissue fit, clipped to [0, 1] |
+| `mask.npy` | `(X, Y, Z)` bool: the brain mask (median-Otsu on the mean b = 0) |
+| `labels.npy` | `(X, Y, Z)` int16: the 84 Desikan-Killiany + subcortical regions (MRtrix `fs_default` order: left 34 cortical then 8 subcortical, then right), 0 elsewhere |
+| `regions.json` | the 84 regions (id, FreeSurfer label, name, hemisphere, lobe) and the 14 lobar groups (7 lobes × 2 hemispheres) |
+| `stop_mask.npy` | `(X, Y, Z)` bool: where a streamline may continue (cerebral and cerebellar white matter, brain stem); leaving it ends the streamline |
+| `mean_b0.npy` | `(X, Y, Z)` float32: the mean b = 0 image, the page's background |
+| `checks/` | `msmt_sample.npz`, a fixed-seed sample of 2,000 voxels' signal, coefficients and fractions (the reference for dmipy-fit#39's fast solver); `sanity_summary.json`; an axial slice with the FOD's principal directions |
+
+## How it was made
+
+* **Reconstruction, dmipy-fit only** (`tools/build_brain_asset.py` in dmrai-lab/disco-space): three-tissue response
+  functions estimated from the data (`three_tissue_response_dhollander16`, Dhollander 2016, selected from the brain
+  mask eroded by 3 passes as MRtrix3's `dwi2response dhollander -erode 3`, the WM response by Tournier 2013's
+  iterative single-fibre selection), then multi-shell multi-tissue CSD (`MultiCompartmentSphericalHarmonicsModel`,
+  Jeurissen 2014, `solver="csd_msmt_torch"`: the batched interior-point solver of dmipy-fit#40, every voxel to a
+  KKT tolerance of 1e-13) at order 8 with the responses' S0 folded in, so the fractions are geometric. The whole
+  brain (71,052 voxels × 485 measurements) took 24 s on a CPU. The dmipy-fit commit is in the manifest.
+  Revision 1 of this dataset held the same fit by `CsdCvxpyOptimizer` (OSQP, 87 minutes on a CPU), whose inexact
+  solutions left negative FOD lobes; revision 2 replaced it with the interior-point solver; revision 3 corrects the
+  response selection: revision 2 selected its WM response from the un-eroded mask by FA, which took 300 noise voxels
+  of FA ≈ 1 at the brain's edge and outside it (131 unlabelled by SynthSeg), so its WM response had 0.77 of white
+  matter's b = 0 and every white-matter voxel's fractions came out 1.2 to 1.3 times too large (median sum 1.24 in
+  cerebral WM). With the eroded mask and Tournier 2013, 282 of the 300 selected voxels lie in cerebral WM and the
+  fit's b = 0 is 0.997 of the measured (IQR 0.992-1.003) in every tissue class.
+* **The sum of the fractions.** Multi-tissue CSD does not constrain WM + GM + CSF to one: each response carries one
+  image-wide b = 0 amplitude while the measured b = 0 varies voxel by voxel (receive field, partial volume, T2), so
+  the sum follows the measured b = 0 (Pearson 0.81 in interior white matter). Median sum 0.90 (IQR 0.80-0.98 in
+  cerebral WM, 0.82-1.04 in cortical GM), 20,177 of 71,052 voxels above one, mostly in the cerebellum (median 1.4,
+  where b = 0 is 1.6-1.8 times the cerebral white matter's) and the brain stem. No smooth field explains it (a cubic
+  polynomial or a 30 mm Gaussian explains 0.3 of the variance of its logarithm), so a consumer that needs shares of
+  a voxel divides by the sum where it exceeds one (the brain Space does, and counts the voxels it did it to), as
+  MRtrix3's `mtnormalise` would after its smooth correction.
+* **Parcellation** (`tools/build_parcellation.py`): SynthSeg `--parc --robust` (Billot et al.) on the T1, a rigid
+  mutual-information registration of the T1 onto the mean b = 0, and a plurality vote of 64 sub-points per diffusion
+  voxel. All 84 nodes are present; per-label volume 578 to 20,656 mm³ (median 4,844).
+
+## Use
+
+```python
+import json, numpy as np
+from huggingface_hub import snapshot_download
+d = snapshot_download("SubstrateCommons/masivar-brain", repo_type="dataset")
+man = json.load(open(f"{d}/manifest.json")); fod = np.load(f"{d}/fod_wm.npy"); fr = np.load(f"{d}/fractions.npy")
+```
+
+The brain Space composes these with the replay packs of `SubstrateCommons/cactus-axons` (white matter) and
+`SubstrateCommons/grey-matter-spheres` (grey matter) through dmipy-sim's phantom route.
+
+Please cite Cai et al. 2021 and the OpenNeuro dataset when you use this.
+
+## Licence
+
+The asset (the FOD field, the fractions, the parcellation and the masks) is distributed under `CC-BY-NC-SA-4.0 OR LicenseRef-Commercial`: see [LICENSING.md](LICENSING.md). Its source, MASiVar sub-cIs1 (OpenNeuro ds003416), is CC0, recorded in `manifest.json` under `source.license`; this asset does not relicense it.

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checks/sanity_summary.json

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+  "fractions": {
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+    "sum_p99": 1.56787109375,
+    "n_wm_gt_half": 22488,
+    "n_mask": 71052
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+    "5": 134,
+    "4": 296,
+    "1": 15438,
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+    "3": 1073,
+    "7": 3
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manifest.json

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+ "subject": "MASiVar sub-cIs1 ses-s1Ax1 run-1xx",
+ "source": {
+  "dataset": "OpenNeuro ds003416",
+  "doi": "10.18112/openneuro.ds003416.v2.0.2",
+  "paper_doi": "10.1002/mrm.28926",
+  "license": "CC0",
+  "scan": "ses-s1Ax1 run-1xx (b1000/1500/2000/2500/3000, n=96 each, PreQual-preprocessed)"
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+  "date": "2026-10-01T15:09:49Z"
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+ "asset_license_url": "https://huggingface.co/datasets/SubstrateCommons/masivar-brain/blob/main/LICENSING.md"
+}

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+      "hemisphere": "right",
+      "lobe": "temporal",
+      "id": 56
+    },
+    {
+      "fs_label": 2016,
+      "name": "parahippocampal",
+      "hemisphere": "right",
+      "lobe": "temporal",
+      "id": 57
+    },
+    {
+      "fs_label": 2017,
+      "name": "paracentral",
+      "hemisphere": "right",
+      "lobe": "frontal",
+      "id": 58
+    },
+    {
+      "fs_label": 2018,
+      "name": "parsopercularis",
+      "hemisphere": "right",
+      "lobe": "frontal",
+      "id": 59
+    },
+    {
+      "fs_label": 2019,
+      "name": "parsorbitalis",
+      "hemisphere": "right",
+      "lobe": "frontal",
+      "id": 60
+    },
+    {
+      "fs_label": 2020,
+      "name": "parstriangularis",
+      "hemisphere": "right",
+      "lobe": "frontal",
+      "id": 61
+    },
+    {
+      "fs_label": 2021,
+      "name": "pericalcarine",
+      "hemisphere": "right",
+      "lobe": "occipital",
+      "id": 62
+    },
+    {
+      "fs_label": 2022,
+      "name": "postcentral",
+      "hemisphere": "right",
+      "lobe": "parietal",
+      "id": 63
+    },
+    {
+      "fs_label": 2023,
+      "name": "posteriorcingulate",
+      "hemisphere": "right",
+      "lobe": "cingulate",
+      "id": 64
+    },
+    {
+      "fs_label": 2024,
+      "name": "precentral",
+      "hemisphere": "right",
+      "lobe": "frontal",
+      "id": 65
+    },
+    {
+      "fs_label": 2025,
+      "name": "precuneus",
+      "hemisphere": "right",
+      "lobe": "parietal",
+      "id": 66
+    },
+    {
+      "fs_label": 2026,
+      "name": "rostralanteriorcingulate",
+      "hemisphere": "right",
+      "lobe": "cingulate",
+      "id": 67
+    },
+    {
+      "fs_label": 2027,
+      "name": "rostralmiddlefrontal",
+      "hemisphere": "right",
+      "lobe": "frontal",
+      "id": 68
+    },
+    {
+      "fs_label": 2028,
+      "name": "superiorfrontal",
+      "hemisphere": "right",
+      "lobe": "frontal",
+      "id": 69
+    },
+    {
+      "fs_label": 2029,
+      "name": "superiorparietal",
+      "hemisphere": "right",
+      "lobe": "parietal",
+      "id": 70
+    },
+    {
+      "fs_label": 2030,
+      "name": "superiortemporal",
+      "hemisphere": "right",
+      "lobe": "temporal",
+      "id": 71
+    },
+    {
+      "fs_label": 2031,
+      "name": "supramarginal",
+      "hemisphere": "right",
+      "lobe": "parietal",
+      "id": 72
+    },
+    {
+      "fs_label": 2032,
+      "name": "frontalpole",
+      "hemisphere": "right",
+      "lobe": "frontal",
+      "id": 73
+    },
+    {
+      "fs_label": 2033,
+      "name": "temporalpole",
+      "hemisphere": "right",
+      "lobe": "temporal",
+      "id": 74
+    },
+    {
+      "fs_label": 2034,
+      "name": "transversetemporal",
+      "hemisphere": "right",
+      "lobe": "temporal",
+      "id": 75
+    },
+    {
+      "fs_label": 2035,
+      "name": "insula",
+      "hemisphere": "right",
+      "lobe": "insula",
+      "id": 76
+    },
+    {
+      "fs_label": 49,
+      "name": "Thalamus",
+      "hemisphere": "right",
+      "lobe": "subcortical",
+      "id": 77
+    },
+    {
+      "fs_label": 50,
+      "name": "Caudate",
+      "hemisphere": "right",
+      "lobe": "subcortical",
+      "id": 78
+    },
+    {
+      "fs_label": 51,
+      "name": "Putamen",
+      "hemisphere": "right",
+      "lobe": "subcortical",
+      "id": 79
+    },
+    {
+      "fs_label": 52,
+      "name": "Pallidum",
+      "hemisphere": "right",
+      "lobe": "subcortical",
+      "id": 80
+    },
+    {
+      "fs_label": 53,
+      "name": "Hippocampus",
+      "hemisphere": "right",
+      "lobe": "subcortical",
+      "id": 81
+    },
+    {
+      "fs_label": 54,
+      "name": "Amygdala",
+      "hemisphere": "right",
+      "lobe": "subcortical",
+      "id": 82
+    },
+    {
+      "fs_label": 58,
+      "name": "Accumbens-area",
+      "hemisphere": "right",
+      "lobe": "subcortical",
+      "id": 83
+    },
+    {
+      "fs_label": 60,
+      "name": "VentralDC",
+      "hemisphere": "right",
+      "lobe": "subcortical",
+      "id": 84
+    }
+  ],
+  "lobes": [
+    "frontal-left",
+    "frontal-right",
+    "parietal-left",
+    "parietal-right",
+    "temporal-left",
+    "temporal-right",
+    "occipital-left",
+    "occipital-right",
+    "cingulate-left",
+    "cingulate-right",
+    "insula-left",
+    "insula-right",
+    "subcortical-left",
+    "subcortical-right"
+  ]
+}

stop_mask.npy

@@ -0,0 +1,3 @@
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+size 350336