diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000000000000000000000000000000000000..bed0738c7eeb449bca98b5d2f33c89a1ee56349a --- /dev/null +++ b/.gitattributes @@ -0,0 +1,60 @@ +*.7z filter=lfs diff=lfs merge=lfs -text +*.arrow filter=lfs diff=lfs merge=lfs -text +*.avro filter=lfs diff=lfs merge=lfs -text +*.bin filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.ckpt filter=lfs diff=lfs merge=lfs -text +*.ftz filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.h5 filter=lfs diff=lfs merge=lfs -text +*.joblib filter=lfs diff=lfs merge=lfs -text +*.lfs.* filter=lfs diff=lfs merge=lfs -text +*.lz4 filter=lfs diff=lfs merge=lfs -text +*.mds filter=lfs diff=lfs merge=lfs -text +*.mlmodel filter=lfs diff=lfs merge=lfs -text +*.model filter=lfs diff=lfs merge=lfs -text +*.msgpack filter=lfs diff=lfs merge=lfs -text +*.npy filter=lfs diff=lfs merge=lfs -text +*.npz filter=lfs diff=lfs merge=lfs -text +*.onnx filter=lfs diff=lfs merge=lfs -text +*.ot filter=lfs diff=lfs merge=lfs -text +*.parquet filter=lfs diff=lfs merge=lfs -text +*.pb filter=lfs diff=lfs merge=lfs -text +*.pickle filter=lfs diff=lfs merge=lfs -text +*.pkl filter=lfs diff=lfs merge=lfs -text +*.pt filter=lfs diff=lfs merge=lfs -text +*.pth filter=lfs diff=lfs merge=lfs -text +*.rar filter=lfs diff=lfs merge=lfs -text +*.safetensors filter=lfs diff=lfs merge=lfs -text +saved_model/**/* filter=lfs diff=lfs merge=lfs -text +*.tar.* filter=lfs diff=lfs merge=lfs -text +*.tar filter=lfs diff=lfs merge=lfs -text +*.tflite filter=lfs diff=lfs merge=lfs -text +*.tgz filter=lfs diff=lfs merge=lfs -text +*.wasm filter=lfs diff=lfs merge=lfs -text +*.xz filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.zst filter=lfs diff=lfs merge=lfs -text +*tfevents* filter=lfs diff=lfs merge=lfs -text +# Audio files - uncompressed +*.pcm filter=lfs diff=lfs merge=lfs -text +*.sam filter=lfs diff=lfs merge=lfs -text +*.raw filter=lfs diff=lfs merge=lfs -text +# Audio files - compressed +*.aac filter=lfs diff=lfs merge=lfs -text +*.flac filter=lfs diff=lfs merge=lfs -text +*.mp3 filter=lfs diff=lfs merge=lfs -text +*.ogg filter=lfs diff=lfs merge=lfs -text +*.wav filter=lfs diff=lfs merge=lfs -text +# Image files - uncompressed +*.bmp filter=lfs diff=lfs merge=lfs -text +*.gif filter=lfs diff=lfs merge=lfs -text +*.png filter=lfs diff=lfs merge=lfs -text +*.tiff filter=lfs diff=lfs merge=lfs -text +# Image files - compressed +*.jpg filter=lfs diff=lfs merge=lfs -text +*.jpeg filter=lfs diff=lfs merge=lfs -text +*.webp 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 diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..5590f7a0e4a6e6761fd5173c74cf030bf1934386 --- /dev/null +++ b/README.md @@ -0,0 +1,384 @@ +--- +license: cc-by-4.0 +pretty_name: OpenMind (preprocessed, NeuroSpin) +task_categories: +- image-feature-extraction +tags: +- 3d +- mri +- neuroimaging +- brain +- medical +- webdataset +- self-supervised-learning +- voxel-based-morphometry +- cat12 +size_categories: +- 10K/val_split.csv +train = OpenMind(root, preprocessing="quasiraw", modality="t1", split="train", apply_mask=True) +val = OpenMind(root, preprocessing="quasiraw", modality="t1", split="val", apply_mask=True) +print(train[0].shape) # (1, 182, 218, 182) + +# Quasi-raw: paired T1w / T2w acquired in the same session +paired = OpenMind(root, modality=("t1", "t2"), group_by="session", split="train") +sample = paired[0] # {"t1": array, "t2": array} + +# CAT12 VBM: grey matter map and ROI morphometry +vbm = OpenMind(root, preprocessing="cat12vbm", split="train", return_morphometry=True) +gm, morphometry = vbm[0] +print(gm.shape, morphometry["total_volumes"]["TIV"]) # (1, 113, 137, 113) ... + +loader = DataLoader(train, batch_size=8, shuffle=True, num_workers=8) +``` + +`nidl` does not read the CAT12 quality ratings (`qc.json`): use the webdataset example of the +`cat12vbm-12.8.2` section to get them. + +## `quasiraw-v2.1.1` + +### Content + +| | | +|---|---| +| Images | 71,490 (T1w 42,941 · T2w 23,935 · FLAIR 4,614) | +| Subjects | 33,738 | +| Source datasets | 787 OpenNeuro datasets | +| Size | 462 GB, 849 shards | +| Image grid | 182 × 218 × 182, 1 mm isotropic, MNI152 space, float32 | + +### Preprocessing + +[brainprep](https://github.com/brainprepdesk/brainprep) `subject-level-quasiraw` (v2.1.1 +container), applied per modality, with the matching MNI152 template (T1 template for T1w, +T2 template for T2w / FLAIR): + +1. Reorientation to the MNI152 orientation. +2. Brain mask with FreeSurfer [SynthStrip](https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/). +3. N4 bias field correction. +4. Resampling to 1 mm isotropic. +5. Linear (affine, 9 DOF) registration to the MNI152 1 mm template. +6. The registration is applied to the bias-corrected image and the brain mask; the image + is then multiplied by the mask (skull-stripped). + +"Quasi-raw" means minimal preprocessing: no non-linear warp, no tissue segmentation, no +intensity standardization across scans. Intensities are those of the bias-corrected scan. + +### Layout + +``` +quasiraw-v2.1.1/ +├── index.json.gz # byte offsets for random access (nidl) +└── / # one folder per OpenNeuro dataset, e.g. ds000001 + └── -NNNNNN.tar # WebDataset shard(s), ≤ ~3 GB each +``` + +Each sample is one image of one (subject, session, run, modality). Its key is +`sub-