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Angelou0516
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TotalSegmentatorMR

Tasks:
Image Segmentation
Modalities:
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Tags:
medical-imaging
whole-body
multi-organ
sequence-independent
nnU-Net
TotalSegmentator
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Upload TotalSegmentatorMR data (batch 1/2)

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  1. README.md +95 -0
  2. s0001/mri.nii.gz +3 -0
  3. s0001/segmentations/adrenal_gland_left.nii.gz +3 -0
  4. s0001/segmentations/adrenal_gland_right.nii.gz +3 -0
  5. s0001/segmentations/aorta.nii.gz +3 -0
  6. s0001/segmentations/autochthon_left.nii.gz +3 -0
  7. s0001/segmentations/autochthon_right.nii.gz +3 -0
  8. s0001/segmentations/brain.nii.gz +3 -0
  9. s0001/segmentations/clavicula_left.nii.gz +3 -0
  10. s0001/segmentations/clavicula_right.nii.gz +3 -0
  11. s0001/segmentations/colon.nii.gz +3 -0
  12. s0001/segmentations/duodenum.nii.gz +3 -0
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  14. s0001/segmentations/femur_left.nii.gz +3 -0
  15. s0001/segmentations/femur_right.nii.gz +3 -0
  16. s0001/segmentations/gallbladder.nii.gz +3 -0
  17. s0001/segmentations/gluteus_maximus_left.nii.gz +3 -0
  18. s0001/segmentations/gluteus_maximus_right.nii.gz +3 -0
  19. s0001/segmentations/gluteus_medius_left.nii.gz +3 -0
  20. s0001/segmentations/gluteus_medius_right.nii.gz +3 -0
  21. s0001/segmentations/gluteus_minimus_left.nii.gz +3 -0
  22. s0001/segmentations/gluteus_minimus_right.nii.gz +3 -0
  23. s0001/segmentations/heart.nii.gz +3 -0
  24. s0001/segmentations/hip_left.nii.gz +3 -0
  25. s0001/segmentations/hip_right.nii.gz +3 -0
  26. s0001/segmentations/humerus_left.nii.gz +3 -0
  27. s0001/segmentations/humerus_right.nii.gz +3 -0
  28. s0001/segmentations/iliac_artery_left.nii.gz +3 -0
  29. s0001/segmentations/iliac_artery_right.nii.gz +3 -0
  30. s0001/segmentations/iliac_vena_left.nii.gz +3 -0
  31. s0001/segmentations/iliac_vena_right.nii.gz +3 -0
  32. s0001/segmentations/iliopsoas_left.nii.gz +3 -0
  33. s0001/segmentations/iliopsoas_right.nii.gz +3 -0
  34. s0001/segmentations/inferior_vena_cava.nii.gz +3 -0
  35. s0001/segmentations/intervertebral_discs.nii.gz +3 -0
  36. s0001/segmentations/kidney_left.nii.gz +3 -0
  37. s0001/segmentations/kidney_right.nii.gz +3 -0
  38. s0001/segmentations/liver.nii.gz +3 -0
  39. s0001/segmentations/lung_left.nii.gz +3 -0
  40. s0001/segmentations/lung_right.nii.gz +3 -0
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  42. s0001/segmentations/portal_vein_and_splenic_vein.nii.gz +3 -0
  43. s0001/segmentations/prostate.nii.gz +3 -0
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  45. s0001/segmentations/scapula_left.nii.gz +3 -0
  46. s0001/segmentations/scapula_right.nii.gz +3 -0
  47. s0001/segmentations/small_bowel.nii.gz +3 -0
  48. s0001/segmentations/spinal_cord.nii.gz +3 -0
  49. s0001/segmentations/spleen.nii.gz +3 -0
  50. s0001/segmentations/stomach.nii.gz +3 -0
README.md ADDED
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+ ---
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+ license: cc-by-nc-sa-2.0
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+ task_categories:
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+ - image-segmentation
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+ modality:
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+ - MRI
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+ language: []
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+ tags:
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+ - medical-imaging
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+ - whole-body
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+ - multi-organ
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+ - sequence-independent
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+ - nnU-Net
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+ - TotalSegmentator
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+ pretty_name: TotalSegmentator MRI v2.0.0
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+ size_categories:
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+ - n<1K
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+ ---
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+
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+ # TotalSegmentator MRI (v2.0.0)
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+
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+ Public release of the **TotalSegmentator MRI** dataset: 616 heterogeneous MRI scans (T1, T2, PD, DIXON-style and other sequences, multiple field strengths, scanners, slice thicknesses, contrast agents) with voxel-wise annotations of **50 anatomical structures** spanning the whole body.
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+
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+ ## Dataset Summary
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+
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+ | Field | Details |
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+ |---|---|
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+ | Modality | MRI (sequence-independent: T1w / T2w / PD / DIXON / mixed) |
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+ | Body Part | Whole-body / multi-organ |
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+ | Structures | 50 anatomical regions per scan |
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+ | Subjects | 616 MRI scans (561 train / 55 internal test, per `meta.csv`) |
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+ | Sources | University Hospital Basel PACS (2011–2023) + Imaging Data Commons |
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+ | Total Size | ~5.8 GB |
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+ | License | CC BY-NC-SA 2.0 (non-commercial) |
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+ | Source | Zenodo: https://zenodo.org/records/14710732 |
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+
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+ The dataset is the MR portion of the study cohort described in the *Radiology* paper. External AMOS and CHAOS test sets referenced by the paper are **not** redistributed here — they live in their own datasets and are referenced by `meta.csv` only.
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+
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+ ## Annotation Pipeline
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+
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+ Ground-truth masks were produced iteratively:
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+ 1. Initial segmentations from public CT/MR models where available.
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+ 2. Manual segmentation of the first 10 patients to bootstrap an internal nnU-Net.
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+ 3. Predicted masks were manually refined; the model was retrained after every additional 125 reviewed patients.
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+ 4. **All annotations were manually reviewed and corrected when needed by a board-certified radiologist with 12 years of experience**, blinded to radiology reports.
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+
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+ A single GT mask volume per scan is provided. There is no "predicted vs. corrected" duality.
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+
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+ ## Data Structure
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+
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+ ```
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+ TotalSegmentatorMR/
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+ ├── meta.csv # split + scanner metadata (semicolon-separated)
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+ └── s{0001..0616}/
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+ ├── mri.nii.gz # MR scan
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+ └── segmentations/
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+ ├── adrenal_gland_left.nii.gz
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+ ├── adrenal_gland_right.nii.gz
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+ ├── aorta.nii.gz
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+ ├── ... # one binary mask per anatomical structure
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+ └── (50 files total)
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+ ```
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+
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+ Each `segmentations/<structure>.nii.gz` is a binary mask aligned to the corresponding `mri.nii.gz`.
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+
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+ ### `meta.csv` columns
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+
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+ `image_id; split; age; gender; institute; study_type; manufacturer; scanner_model; slice_thickness; scanning_sequence; repetition_time; echo_time; magnetic_field_strength; source`
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+
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+ The `split` column encodes train/test partitioning; `source` distinguishes Basel PACS vs IDC provenance.
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+
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+ ## Versioning
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+
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+ - **v2.0.0** (current, this upload) — 616 scans, 50 anatomical regions. `subcutaneous_fat`, `torso_fat`, `skeletal_muscle`, and `face_region` were moved into separate subtask models (`tissue_types_mr`, `face_mr`).
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+ - v1.0.0 — 298 scans, 56 anatomical regions.
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+
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+ ## Citation
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+
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+ ```bibtex
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+ @article{akinci2025totalsegmentatormr,
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+ title = {{TotalSegmentator MRI}: Robust Sequence-independent Segmentation of Multiple Anatomic Structures in {MRI}},
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+ author = {Akinci D'Antonoli, Tugba and Berger, Lucas K. and Indrakanti, Ashraya K. and Vishwanathan, Nathan and Wei{\ss}, Jakob and Jung, Matthias and Berkarda, Zeynep and Rau, Alexander and Reisert, Marco and K{\"u}stner, Thomas and Walter, Annette and Merkle, Elmar M. and Boll, Daniel T. and Breit, Hanns-Christian and Nicoli, Andrea P. and Segeroth, Martin and Cyriac, Joshy and Yang, Shan and Wasserthal, Jakob},
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+ journal = {Radiology},
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+ year = {2025},
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+ doi = {10.1148/radiol.241613}
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+ }
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+
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+ @article{wasserthal2023totalsegmentator,
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+ title = {{TotalSegmentator}: Robust Segmentation of 104 Anatomic Structures in {CT} Images},
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+ author = {Wasserthal, Jakob and Breit, Hanns-Christian and Meyer, Manfred T. and Pradella, Maurice and Hinck, Daniel and Sauter, Alexander W. and Heye, Tobias and Boll, Daniel T. and Cyriac, Joshy and Yang, Shan and Bach, Michael and Segeroth, Martin},
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+ journal = {Radiology: Artificial Intelligence},
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+ year = {2023},
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+ doi = {10.1148/ryai.230024}
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+ }
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+ ```
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