Commit ·
afe5589
0
Parent(s):
Squash history: one commit holding the current files
Browse filesThis view is limited to 50 files because it contains too many changes. See raw diff
- .gitattributes +1463 -0
- README.md +116 -0
- STATUS.md +16 -0
- certificate/disco-block-0000.json +82 -0
- certificate/disco-block-0000.rpk +3 -0
- certificate/disco-block-0000.run/events.jsonl +50 -0
- certificate/disco-block-0000.run/manifest.json +39 -0
- certificate/disco-block-0000.run/summary.json +19 -0
- certificate/disco.json +0 -0
- disco/columns/band_block.p000.safetensors +3 -0
- disco/columns/band_block.p001.safetensors +3 -0
- disco/columns/blt_b0.p000.safetensors +3 -0
- disco/columns/blt_b0.p001.safetensors +3 -0
- disco/columns/blt_b0.p002.safetensors +3 -0
- disco/columns/blt_b0.p003.safetensors +3 -0
- disco/columns/blt_band_scale.safetensors +3 -0
- disco/columns/blt_endpoint.p000.safetensors +3 -0
- disco/columns/blt_endpoint.p001.safetensors +3 -0
- disco/columns/blt_start.p000.safetensors +3 -0
- disco/columns/blt_start.p001.safetensors +3 -0
- disco/columns/comp_static.p000.safetensors +3 -0
- disco/columns/comp_static.p001.safetensors +3 -0
- disco/columns/pos_band_scale.safetensors +3 -0
- disco/columns/pos_x_b0.p000.safetensors +3 -0
- disco/columns/pos_x_b0.p001.safetensors +3 -0
- disco/columns/pos_x_b0.p002.safetensors +3 -0
- disco/columns/pos_x_b0.p003.safetensors +3 -0
- disco/columns/pos_x_b0.p004.safetensors +3 -0
- disco/columns/pos_x_b0.p005.safetensors +3 -0
- disco/columns/pos_x_b1.p000.safetensors +3 -0
- disco/columns/pos_x_b1.p001.safetensors +3 -0
- disco/columns/pos_x_b1.p002.safetensors +3 -0
- disco/columns/pos_x_b1.p003.safetensors +3 -0
- disco/columns/pos_x_b2.p000.safetensors +3 -0
- disco/columns/pos_x_b2.p001.safetensors +3 -0
- disco/columns/pos_x_b2.p002.safetensors +3 -0
- disco/columns/pos_x_b2.p003.safetensors +3 -0
- disco/columns/pos_x_b2.p004.safetensors +3 -0
- disco/columns/pos_x_b2.p005.safetensors +3 -0
- disco/columns/pos_x_b3.p000.safetensors +3 -0
- disco/columns/pos_x_b3.p001.safetensors +3 -0
- disco/columns/pos_x_b3.p002.safetensors +3 -0
- disco/columns/pos_x_b3.p003.safetensors +3 -0
- disco/columns/pos_x_b3.p004.safetensors +3 -0
- disco/columns/pos_x_b3.p005.safetensors +3 -0
- disco/columns/pos_x_b3.p006.safetensors +3 -0
- disco/columns/pos_x_b3.p007.safetensors +3 -0
- disco/columns/pos_x_b3.p008.safetensors +3 -0
- disco/columns/pos_x_b3.p009.safetensors +3 -0
- disco/columns/pos_x_b3.p010.safetensors +3 -0
.gitattributes
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| 1 |
+
*.7z filter=lfs diff=lfs merge=lfs -text
|
| 2 |
+
*.arrow filter=lfs diff=lfs merge=lfs -text
|
| 3 |
+
*.avro filter=lfs diff=lfs merge=lfs -text
|
| 4 |
+
*.bin filter=lfs diff=lfs merge=lfs -text
|
| 5 |
+
*.bz2 filter=lfs diff=lfs merge=lfs -text
|
| 6 |
+
*.ckpt filter=lfs diff=lfs merge=lfs -text
|
| 7 |
+
*.ftz filter=lfs diff=lfs merge=lfs -text
|
| 8 |
+
*.gz filter=lfs diff=lfs merge=lfs -text
|
| 9 |
+
*.h5 filter=lfs diff=lfs merge=lfs -text
|
| 10 |
+
*.joblib filter=lfs diff=lfs merge=lfs -text
|
| 11 |
+
*.lfs.* filter=lfs diff=lfs merge=lfs -text
|
| 12 |
+
*.lz4 filter=lfs diff=lfs merge=lfs -text
|
| 13 |
+
*.mds filter=lfs diff=lfs merge=lfs -text
|
| 14 |
+
*.mlmodel filter=lfs diff=lfs merge=lfs -text
|
| 15 |
+
*.model filter=lfs diff=lfs merge=lfs -text
|
| 16 |
+
*.msgpack filter=lfs diff=lfs merge=lfs -text
|
| 17 |
+
*.npy filter=lfs diff=lfs merge=lfs -text
|
| 18 |
+
*.npz filter=lfs diff=lfs merge=lfs -text
|
| 19 |
+
*.onnx filter=lfs diff=lfs merge=lfs -text
|
| 20 |
+
*.ot filter=lfs diff=lfs merge=lfs -text
|
| 21 |
+
*.parquet filter=lfs diff=lfs merge=lfs -text
|
| 22 |
+
*.pb filter=lfs diff=lfs merge=lfs -text
|
| 23 |
+
*.pickle filter=lfs diff=lfs merge=lfs -text
|
| 24 |
+
*.pkl filter=lfs diff=lfs merge=lfs -text
|
| 25 |
+
*.pt filter=lfs diff=lfs merge=lfs -text
|
| 26 |
+
*.pth filter=lfs diff=lfs merge=lfs -text
|
| 27 |
+
*.rar filter=lfs diff=lfs merge=lfs -text
|
| 28 |
+
*.safetensors filter=lfs diff=lfs merge=lfs -text
|
| 29 |
+
saved_model/**/* filter=lfs diff=lfs merge=lfs -text
|
| 30 |
+
*.tar.* filter=lfs diff=lfs merge=lfs -text
|
| 31 |
+
*.tar filter=lfs diff=lfs merge=lfs -text
|
| 32 |
+
*.tflite filter=lfs diff=lfs merge=lfs -text
|
| 33 |
+
*.tgz filter=lfs diff=lfs merge=lfs -text
|
| 34 |
+
*.wasm filter=lfs diff=lfs merge=lfs -text
|
| 35 |
+
*.xz filter=lfs diff=lfs merge=lfs -text
|
| 36 |
+
*.zip filter=lfs diff=lfs merge=lfs -text
|
| 37 |
+
*.zst filter=lfs diff=lfs merge=lfs -text
|
| 38 |
+
*tfevents* filter=lfs diff=lfs merge=lfs -text
|
| 39 |
+
# Audio files - uncompressed
|
| 40 |
+
*.pcm filter=lfs diff=lfs merge=lfs -text
|
| 41 |
+
*.sam filter=lfs diff=lfs merge=lfs -text
|
| 42 |
+
*.raw filter=lfs diff=lfs merge=lfs -text
|
| 43 |
+
# Audio files - compressed
|
| 44 |
+
*.aac filter=lfs diff=lfs merge=lfs -text
|
| 45 |
+
*.flac filter=lfs diff=lfs merge=lfs -text
|
| 46 |
+
*.mp3 filter=lfs diff=lfs merge=lfs -text
|
| 47 |
+
*.ogg filter=lfs diff=lfs merge=lfs -text
|
| 48 |
+
*.wav filter=lfs diff=lfs merge=lfs -text
|
| 49 |
+
# Image files - uncompressed
|
| 50 |
+
*.bmp filter=lfs diff=lfs merge=lfs -text
|
| 51 |
+
*.gif filter=lfs diff=lfs merge=lfs -text
|
| 52 |
+
*.png filter=lfs diff=lfs merge=lfs -text
|
| 53 |
+
*.tiff filter=lfs diff=lfs merge=lfs -text
|
| 54 |
+
# Image files - compressed
|
| 55 |
+
*.jpg filter=lfs diff=lfs merge=lfs -text
|
| 56 |
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*.jpeg filter=lfs diff=lfs merge=lfs -text
|
| 57 |
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*.webp filter=lfs diff=lfs merge=lfs -text
|
| 58 |
+
# Video files - compressed
|
| 59 |
+
*.mp4 filter=lfs diff=lfs merge=lfs -text
|
| 60 |
+
*.webm filter=lfs diff=lfs merge=lfs -text
|
| 61 |
+
substrate/DiSCo_Strands_Trajectories.tck filter=lfs diff=lfs merge=lfs -text
|
| 62 |
+
certificate/ground-truth-block-0000.rpk filter=lfs diff=lfs merge=lfs -text
|
| 63 |
+
blocks/ground-truth/block-0000.rpk filter=lfs diff=lfs merge=lfs -text
|
| 64 |
+
certificate/disco-block-0000.rpk filter=lfs diff=lfs merge=lfs -text
|
| 65 |
+
blocks/disco/block-0001.rpk filter=lfs diff=lfs merge=lfs -text
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| 66 |
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| 840 |
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| 1410 |
+
blocks/disco/block-1343.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1411 |
+
blocks/disco/block-1344.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1412 |
+
blocks/disco/block-1345.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1413 |
+
blocks/disco/block-1349.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1414 |
+
blocks/disco/block-1346.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1415 |
+
blocks/disco/block-1353.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1416 |
+
blocks/disco/block-1350.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1417 |
+
blocks/disco/block-1354.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1418 |
+
blocks/disco/block-1355.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1419 |
+
blocks/disco/block-1356.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1420 |
+
blocks/disco/block-1351.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1421 |
+
blocks/disco/block-1357.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1422 |
+
blocks/disco/block-1352.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1423 |
+
blocks/disco/block-1358.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1424 |
+
blocks/disco/block-1359.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1425 |
+
blocks/disco/block-1362.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1426 |
+
blocks/disco/block-1360.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1427 |
+
blocks/disco/block-1361.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1428 |
+
blocks/disco/block-1363.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1429 |
+
blocks/disco/block-1364.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1430 |
+
blocks/disco/block-1365.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1431 |
+
blocks/disco/block-1368.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1432 |
+
blocks/disco/block-1366.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1433 |
+
blocks/disco/block-1369.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1434 |
+
blocks/disco/block-1367.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1435 |
+
blocks/disco/block-1370.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1436 |
+
blocks/disco/block-1371.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1437 |
+
blocks/disco/block-1377.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1438 |
+
blocks/disco/block-1372.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1439 |
+
blocks/disco/block-1373.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1440 |
+
blocks/disco/block-1378.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1441 |
+
blocks/disco/block-1374.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1442 |
+
blocks/disco/block-1379.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1443 |
+
blocks/disco/block-1380.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1444 |
+
blocks/disco/block-1375.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1445 |
+
blocks/disco/block-1381.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1446 |
+
blocks/disco/block-1382.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1447 |
+
blocks/disco/block-1376.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1448 |
+
blocks/disco/block-1389.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1449 |
+
blocks/disco/block-1383.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1450 |
+
blocks/disco/block-1390.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1451 |
+
blocks/disco/block-1384.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1452 |
+
blocks/disco/block-1391.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1453 |
+
blocks/disco/block-1385.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1454 |
+
blocks/disco/block-1392.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1455 |
+
blocks/disco/block-1393.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1456 |
+
blocks/disco/block-1386.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1457 |
+
blocks/disco/block-1394.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1458 |
+
blocks/disco/block-1387.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1459 |
+
blocks/disco/block-1395.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1460 |
+
blocks/disco/block-1388.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1461 |
+
blocks/disco/block-1396.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1462 |
+
blocks/disco/block-1398.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
| 1463 |
+
blocks/disco/block-1397.p1.rpk filter=lfs diff=lfs merge=lfs -text
|
README.md
ADDED
|
@@ -0,0 +1,116 @@
|
|
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|
|
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|
|
|
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|
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|
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|
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|
|
|
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|
|
|
|
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|
|
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|
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|
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|
|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
|
|
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|
|
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|
|
|
|
|
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|
|
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|
|
|
|
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|
|
|
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|
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|
|
|
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|
|
|
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|
|
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|
|
|
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|
|
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|
|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
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|
|
|
|
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|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: cc-by-4.0
|
| 3 |
+
pretty_name: DiSCo replay phantom
|
| 4 |
+
tags:
|
| 5 |
+
- diffusion-mri
|
| 6 |
+
- monte-carlo
|
| 7 |
+
- replay-pack
|
| 8 |
+
- tractography-phantom
|
| 9 |
+
---
|
| 10 |
+
|
| 11 |
+
# DiSCo as a replay phantom
|
| 12 |
+
|
| 13 |
+
The DiSCo substrate (Rafael-Patino, Girard, Truffet, Pizzolato, Caruyer, Thiran, *The diffusion-simulated
|
| 14 |
+
connectivity (DiSCo) dataset*, Data in Brief 38 (2021) 107429, doi:10.1016/j.dib.2021.107429; data
|
| 15 |
+
doi:10.17632/fgf86jdfg6.3, CC BY 4.0) walked once and stored as a replay pack, so that any acquisition a human
|
| 16 |
+
scanner can play is a replay of the same walk, voxel by voxel on the dataset's own 40³ grid of 25 µm voxels, with
|
| 17 |
+
a per-voxel Monte-Carlo certificate. DiSCo published one acquisition of this substrate; this dataset is the
|
| 18 |
+
substrate itself in replayable form: the same 12,196 strands, two tubes per strand (the listed inner diameter and
|
| 19 |
+
the outer tube at 1/0.7 of it), the dataset's diffusivity in both pools (0.6e-9 m²/s), intra water inside the
|
| 20 |
+
inner tube and extra water outside the outer one, walked for 100 ms with every tier (positions, occupancy, wall
|
| 21 |
+
contact, the strand field along the path).
|
| 22 |
+
|
| 23 |
+
## Use me
|
| 24 |
+
|
| 25 |
+
**Install** dmipy-sim from its main branch (the reader lives there); the dataset is public, no login is needed:
|
| 26 |
+
|
| 27 |
+
```
|
| 28 |
+
pip install "git+https://github.com/dmrai-lab/dmipy-sim@main" "huggingface_hub>=0.25"
|
| 29 |
+
```
|
| 30 |
+
|
| 31 |
+
**1. You want images and no compute.** `disco/reference/` holds pre-replayed volumes on the 40³ grid as S/S0
|
| 32 |
+
NIfTI with their gradient tables: DiSCo's own 364-measurement protocol as bare diffusion (the dataset's own
|
| 33 |
+
simulation) and with white matter at 3 T and 7 T (T2 per pool, surface relaxivity, the sheath's susceptibility),
|
| 34 |
+
four other acquisitions (a clinical b = 1000 shell, a three-shell research scheme, a Connectome 2.0 b = 6000
|
| 35 |
+
shell, a 50 Hz OGSE), the per-voxel floor, the record of what each was read with, the comparison with the
|
| 36 |
+
dataset's own images, and tractography scores. Read its `README.md` first.
|
| 37 |
+
|
| 38 |
+
**2. You want to replay your own acquisition.** Open the pack by reference; nothing is downloaded whole, every byte
|
| 39 |
+
read is one the replay uses (HTTP range reads of the columnar layout under `disco/`):
|
| 40 |
+
|
| 41 |
+
```python
|
| 42 |
+
from dmipy_sim.replay import ReplayPack
|
| 43 |
+
from dmipy_sim import sequences
|
| 44 |
+
from dmipy_sim.spec.tissue import Tissue
|
| 45 |
+
|
| 46 |
+
pack = ReplayPack.open("hf://SubstrateCommons/disco-replay/disco") # 150 M walkers, 31,802 voxels; ~0 bytes so far
|
| 47 |
+
seq = sequences.pgse([[1, 0, 0], [0, 0, 1]], 0.0102, 0.0167, bvalues=[1e9, 1e9], TE=0.0535) # SI: s/m², s; any grid, any TE ≤ 100 ms
|
| 48 |
+
|
| 49 |
+
print(pack.plan(seq)) # bands, tiers, bytes: decided before any transfer
|
| 50 |
+
view = pack.view(K=32, voxels=[(20, 20, 20)]) # one voxel's rows at 32 bands (~1 MB): an ordinary ReplayPack
|
| 51 |
+
S = view.replay(seq) # bare diffusion, the dataset's own physics
|
| 52 |
+
wm = Tissue(T2={"intra": 0.05, "extra": 0.055, "myelin": 0.01}, rho=1.16e-6, chi_iso=-1e-7, chi_aniso=-1e-7)
|
| 53 |
+
view = pack.view(K=32, modes=8, contact=True, voxels=[(20, 20, 20)]) # the tiers the physics needs
|
| 54 |
+
S_3T = view.replay(seq, tissue=wm, scanner=3.0) # relaxation, wall contact, the sheath field at 3 T
|
| 55 |
+
|
| 56 |
+
from dmipy_sim.replay.study import Acquisition, Protocol, Study
|
| 57 |
+
study = Study(Protocol([Acquisition(seq)]), tissues=[None, wm], scanners=[None, 3.0, 7.0], pairs=[(0, 0), (1, 1), (1, 2)])
|
| 58 |
+
S, floor, plan = pack.image(study) # the whole grid: one pass over the rows, every pair from it
|
| 59 |
+
```
|
| 60 |
+
|
| 61 |
+
`S` is `(pairs, 40, 40, 40, measurements)`, NaN where the pack holds no walkers; `floor` the split-half floor of
|
| 62 |
+
each volume, measured in the same pass. A study names a protocol (sequences, each in a pose), the tissues and the
|
| 63 |
+
scanners; the bands are contracted once per acquisition and every tissue and scanner is arithmetic on the result. A replay returns the signal as measured (with the relaxation decay at TE when a tissue carries
|
| 64 |
+
a T2); divide by a b = 0 measurement of the same setting for S/S0, as the reference volumes are. A pass over all rows streams 20 to 100 GB depending on the tiers (about 10 to 25 minutes at
|
| 65 |
+
50-75 MB/s) and needs a GPU for the sums; a voxel takes a second. The replay knobs are three objects, each
|
| 66 |
+
stated once: `tissue` (a `Tissue`, or `pack.nominal` for the spec's values), `scanner` (a field in tesla or a
|
| 67 |
+
catalogue scanner), `orientation`. Nothing is applied silently: the default is bare diffusion. The
|
| 68 |
+
[replay guide](https://github.com/dmrai-lab/dmipy-sim/tree/main/docs/replay-guide) in dmipy-sim is the manual:
|
| 69 |
+
one page per object, the table of what each knob touches and which channel it needs, images by reference, and
|
| 70 |
+
a [DiSCo recipe](https://github.com/dmrai-lab/dmipy-sim/blob/main/docs/replay-guide/recipes/disco.md).
|
| 71 |
+
|
| 72 |
+
**3. You want the walkers themselves.** `disco/` is the lossless form of the pack: every walker of the fill, in
|
| 73 |
+
columns (`disco/columns/*.safetensors`), with nothing requantised; `pack.view(...)` returns any voxels' rows as an
|
| 74 |
+
ordinary `ReplayPack`, and a top-up (a later pass) appends its rows to `disco/columns`. The embedded spec cites the
|
| 75 |
+
strand file at `substrate/DiSCo_Strands_Trajectories.tck`: replay from the dataset's directory, or copy
|
| 76 |
+
`substrate/` under `$DMIPY_SIM_SURFACE_DIR`.
|
| 77 |
+
|
| 78 |
+
## What is certified
|
| 79 |
+
|
| 80 |
+
| | |
|
| 81 |
+
|---|---|
|
| 82 |
+
| state | pass 1 complete (0.16 of the plan, 1,399 shards, 1.5e8 walkers, certified floor median 0.033) + the repair of 332 voxels whose pool the plan had clipped (dmipy-sim#295; `columnar.repair` in `disco/manifest.json`); pass 2, the 0.84 top-up to the 0.008 floor, is held |
|
| 83 |
+
| validation | DiSCo's own protocol replayed against the dataset's noise-free images: correlation 0.989 / 0.990 / 0.988 / 0.981 per shell, per-voxel r.m.s. 0.013 against the certified floor 0.035; a uniform +1 % of S0 because the dataset's tubes are triangle meshes (inner volume 0.953 of the pack's); the replay scores 0.91 on the dataset's connectome through a CSD + probabilistic tracking pipeline, where the dataset's own images score 0.905 |
|
| 84 |
+
| walk | 100 ms gradient-on budget; K = 256 bands (1.28 kHz: every human scanner class at ε = 5e-3), the bands at 16 bits below mode 16 and 8 bits above, nanometre reconstruction; 3,349 saves set by the Connectome 2.0 envelope |
|
| 85 |
+
| tiers | C0 positions, C1 occupancy (static, impermeable), C2 wall contact, C3 the strand field along the path (32 modes, refocusing depth 16); the sheath between the tubes holds no water and is the susceptibility source |
|
| 86 |
+
| field | the exact field of every segment within 18 µm in closed form, the rest through a far grid on 2.5 µm nodes (read error 0.08 % of the field at walker positions); checked against an independent k-space route to 0.03-0.22 % (`substrate/far_field_check.txt`) |
|
| 87 |
+
| outside | voxels farther than 46 µm from every strand hold free extra water and carry no walkers |
|
| 88 |
+
| limits | no myelin water (a multi-echo replay sees two pools where white matter has three); refocusing depth 8 for the field channel; the band and envelope above |
|
| 89 |
+
|
| 90 |
+
## Layout
|
| 91 |
+
|
| 92 |
+
```
|
| 93 |
+
disco/ THE PACK, lossless, in columns (152.8 M rows, 187.7 GB in 237 parts): manifest.json (meta +
|
| 94 |
+
every column's byte layout), index.json (row range per voxel and pool), columns/*.safetensors;
|
| 95 |
+
a top-up appends to columns/
|
| 96 |
+
disco/moments/ the shape-moment layout contracted from disco/ (its manifest names disco/manifest.json's sha256)
|
| 97 |
+
disco/reference/ pre-replayed volumes, their records, the comparison with DiSCo, tractography scores, a card
|
| 98 |
+
manifest.json the fill's recipe: substrate, grid, walk, codec, plan, variants, code commit
|
| 99 |
+
plan/ walkers per voxel per pool; the 1,399 voxel blocks and their seeds
|
| 100 |
+
substrate/ DiSCo's strand files, unchanged (SOURCE.md: provenance and hashes); the far field grid
|
| 101 |
+
certificate/ the fill's measured certificate (disco.json: a scaled block, the full battery; every block
|
| 102 |
+
inherits it), with the certifying block's pack and the record of its walk
|
| 103 |
+
STATUS.md, worker/ the fill's status page at the end of pass 1, and the worker
|
| 104 |
+
```
|
| 105 |
+
|
| 106 |
+
## Contributing compute
|
| 107 |
+
|
| 108 |
+
`worker/README.md`: one process fills blocks in a pipeline, claims by file, no scheduler; every shard records the
|
| 109 |
+
code commit, the seed and the sha256 of what it uploaded, and carries the record of its run, and a finished pass
|
| 110 |
+
is appended to `disco/columns`. Pass 1 was walked by five machines (a GH200, three L40S, a Kaggle T4) in 151
|
| 111 |
+
GPU-hours over two days.
|
| 112 |
+
|
| 113 |
+
## Attribution
|
| 114 |
+
|
| 115 |
+
Substrate: Rafael-Patino et al. 2021 (CC BY 4.0). Replay packs: dmipy-sim (dmrai-lab), replay-pack-spec.
|
| 116 |
+
Cite the dataset paper for the substrate and the replay paper for the packs.
|
STATUS.md
ADDED
|
@@ -0,0 +1,16 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# Fill status — 2026-09-17 16:07 UTC
|
| 2 |
+
|
| 3 |
+
pass 1 (0.16 of the plan): 1399 / 1399 blocks, 147.4 M walkers done, 0.0 M to go — 0 min at the last 1 h's rate
|
| 4 |
+
rate: 23.0 blocks/h, 2.52 M walkers/h; hub: 1399 shards, 188.1 GB; commits in the last hour 36 / 128 (blocks 23, claims 5, heartbeats 7, other 1)
|
| 5 |
+
|
| 6 |
+
| contributor | status | shards | walkers | blocks/h | ms/walker | GPU h | in flight |
|
| 7 |
+
|---|---|---|---|---|---|---|---|
|
| 8 |
+
| GH200 | between blocks | 737 (+4 whole) | 79.73 M | 10.0 | 1.6 | 41.3 | — |
|
| 9 |
+
| L40S | between blocks | 403 | 43.01 M | 13.0 | 3.4 | 47.7 | — |
|
| 10 |
+
| Modal T4 | idle | 167 | 17.15 M | 0.0 | 4.8 | 26.7 | — |
|
| 11 |
+
| Lightning T4 | idle | 73 | 7.83 M | 0.0 | 2.9 | 7.2 | — |
|
| 12 |
+
| Kaggle T4 | idle | 19 | 1.85 M | 0.0 | 32.4 | 17.7 | — |
|
| 13 |
+
|
| 14 |
+
status: live = a claim with a fresh heartbeat; between blocks = no claim, a shard within the last 45 min; idle = nothing for longer; stale = a claim without a heartbeat for over 45 min (a dead worker's; released by the next worker that claims). GPU h = walk + pack time of the shards; ms/walker = walk time per walker at the block's scale.
|
| 15 |
+
|
| 16 |
+
Written by `python -m dmipy_sim.fill.status --publish` from the repository's own files.
|
certificate/disco-block-0000.json
ADDED
|
@@ -0,0 +1,82 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
|
|
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|
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|
|
|
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|
|
|
| 1 |
+
{
|
| 2 |
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"block": 0,
|
| 3 |
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"variant": "disco",
|
| 4 |
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"devices": [
|
| 5 |
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"cuda:0"
|
| 6 |
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],
|
| 7 |
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"commit": "708f50b",
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| 8 |
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| 9 |
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| 11 |
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| 12 |
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| 14 |
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| 15 |
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| 16 |
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|
| 17 |
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| 18 |
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| 19 |
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| 20 |
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| 21 |
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10
|
| 22 |
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| 23 |
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| 24 |
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"seed": 1000,
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| 25 |
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| 26 |
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| 29 |
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| 30 |
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|
| 31 |
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| 32 |
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|
| 33 |
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"sha256": "c8537e8d9fcf7418f21e037ab250b46294323290ef71f7ab6f5e4913ce694d77",
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| 38 |
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"certificate": {
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| 39 |
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| 40 |
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| 41 |
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| 42 |
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| 43 |
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| 46 |
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| 50 |
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| 53 |
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| 54 |
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| 55 |
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"id": "20260915T152215-build_replay_pack-3513558",
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| 56 |
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"walk": {
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| 62 |
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"id": "20260915T151850-walk_spec-3509400",
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| 63 |
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"producer": "walk_spec",
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| 64 |
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"status": "ok",
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| 65 |
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"started": "2026-09-15T15:18:50.717Z",
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| 66 |
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| 79 |
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| 80 |
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| 81 |
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"finished": "2026-09-15T15:30:12Z"
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| 82 |
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|
certificate/disco-block-0000.rpk
ADDED
|
@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:c8537e8d9fcf7418f21e037ab250b46294323290ef71f7ab6f5e4913ce694d77
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| 3 |
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size 251053495
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certificate/disco-block-0000.run/events.jsonl
ADDED
|
@@ -0,0 +1,50 @@
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|
| 1 |
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{"t": "2026-09-15T15:18:50.717Z", "kind": "start", "producer": "walk_spec", "resumed": false}
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{"t": "2026-09-15T15:18:53.099Z", "kind": "phase", "name": "seeding intra", "wanted": 19720}
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{"t": "2026-09-15T15:19:00.783Z", "kind": "resource", "elapsed_s": 10.066017627716064, "rss_bytes": 2483224576, "host_available_bytes": 408838078464, "cgroup_bytes": null, "cgroup_max_bytes": null, "devices": [{"device": "cuda:0", "bytes_in_use": 901663744, "peak_bytes_in_use": 1976055808, "bytes_limit": 20403191808}], "where": ["_stride_tricks_impl.py:477 _broadcast_arrays_dispatcher", "_function_base_impl.py:5260 meshgrid", "seeding.py:133 <listcomp>", "seeding.py:133 _clip_segments_to_voxels", "seeding.py:174 fill_swept_by_voxel", "walk.py:337 seeds"]}
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{"t": "2026-09-15T15:19:09.598Z", "kind": "phase", "name": "walk extra", "n_walkers": 180307, "adaptive_steps": true}
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{"t": "2026-09-15T15:19:10.788Z", "kind": "resource", "elapsed_s": 20.07173228263855, "rss_bytes": 4355391488, "host_available_bytes": 401924161536, "cgroup_bytes": null, "cgroup_max_bytes": null, "devices": [{"device": "cuda:0", "bytes_in_use": 3621816320, "peak_bytes_in_use": 5506517504, "bytes_limit": 20403191808}], "where": ["compiler.py:353 backend_compile_and_load", "profiler.py:420 wrapper", "compiler.py:737 _compile_and_write_cache", "compiler.py:469 compile_or_get_cached", "pxla.py:1516 _cached_compilation", "pxla.py:1733 from_hlo"]}
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{"t": "2026-09-15T15:19:41.613Z", "kind": "progress", "phase": "walk extra", "done": 46730.36727381308, "total": 180307.0, "unit": "walkers", "rate_per_s": 1556.7388836614593, "eta_s": 85.80541934689384, "elapsed_s": 50.89633750915527}
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| 16 |
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{"t": "2026-09-15T15:19:51.620Z", "kind": "progress", "phase": "walk extra", "done": 65840.54941773663, "total": 180307.0, "unit": "walkers", "rate_per_s": 1644.9842730835558, "eta_s": 69.58513370325038, "elapsed_s": 60.903254985809326}
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{"t": "2026-09-15T15:20:00.791Z", "kind": "resource", "elapsed_s": 70.0747754573822, "rss_bytes": 17727881216, "host_available_bytes": 379610660864, "cgroup_bytes": null, "cgroup_max_bytes": null, "devices": [{"device": "cuda:0", "bytes_in_use": 3764889088, "peak_bytes_in_use": 6591974400, "bytes_limit": 20403191808}], "where": ["adaptive.py:292 simulate_trajectories_adaptive", "walk.py:397 _walk_bundle", "walk.py:116 walk_spec", "disco_fill.py:158 walk_block", "disco_fill.py:417 main", "disco_fill.py:447 <module>"]}
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| 20 |
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{"t": "2026-09-15T15:20:11.133Z", "kind": "spool", "name": "extra-batch-0000", "bytes": 9716000416}
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