README.md

metadata

license: cc-by-nc-sa-4.0
task_categories:
  - image-segmentation
tags:
  - medical
  - brain
  - ultrasound
  - mri
  - 3d
  - intraoperative
  - glioma
pretty_name: RESECT + RESECT-SEG (intra-operative brain tumor ultrasound)
dataset_info:
  config_name: preview
  features:
    - name: case_id
      dtype: string
    - name: task
      dtype: string
    - name: structure
      dtype: string
    - name: modality
      dtype: string
    - name: timepoint
      dtype: string
    - name: image_file
      dtype: string
    - name: mask_file
      dtype: string
    - name: num_slices
      dtype: int32
    - name: preview_slice
      dtype: int32
    - name: spacing_mm
      list: float32
    - name: image
      dtype: image
    - name: mask
      dtype: image
    - name: overlay
      dtype: image
  splits:
    - name: train
      num_bytes: 24232816
      num_examples: 181
  download_size: 24222537
  dataset_size: 24232816
configs:
  - config_name: preview
    data_files:
      - split: train
        path: preview/train-*

RESECT + RESECT-SEG

Combined re-host of the RESECT image database (Xiao et al. 2017) and the RESECT-SEG "All-Labels" segmentations (Behboodi et al. 2024, OSF jv8bk v1 2024-02-15) — 23 low-grade glioma (WHO grade II) resections at St. Olavs University Hospital, Trondheim (2011-2016). Pre-operative MRI (Gd-T1w, T2-FLAIR, 1 mm iso) and reconstructed 3D intra-operative B-mode ultrasound at three timepoints (before / during / after resection; per-case isotropic grids, 0.14-0.27 mm). Case IDs are Case1-8, 11-19, 21, 23-27 (9, 10, 20, 22 were never released).

Annotated tasks (181 image-mask pairs, train.jsonl)

task	structure	volume	pairs	note
tumor-us-before	tumor	US before	23	primary CuRIOUS 2022 task
resection_cavity-us-during	resection cavity	US during	21	Case11+15 absent (blood-filled cavity, border indistinguishable)
resection_cavity-us-after	resection cavity	US after	22	Case11 absent
tumor-flair	tumor	pre-op FLAIR	23	int16 {0,1} masks
sulci-us-{before,during,after}	sulci	US x3	23+23+23
falx-us-{before,during,after}	cerebral falx	US x3	8+7+8	only Cases 2,12,14,15,19,21,23,26; during missing for 26

Every mask sits on the exact native grid of its image (identical shape and affine). Masks are binary {0,1} uint8 (FLAIR-tumor: int16). The 23 Gd-T1w volumes carry no annotations (context only). An absent mask file means the structure was not annotated for that volume — unlike the frozen CuRIOUS 2022 release (OSF 6y4db), which shipped 3 of these as all-zero volumes. The jv8bk masks are the authors' recommended, revised tier (not voxel-identical to 6y4db).

Layout

dataset/Case{N}/   Case{N}-{T1,FLAIR,US-before,US-during,US-after}.nii.gz + all masks
landmarks/Case{N}/ MRI<->US / US<->US homologous landmark .tag files (registration)
train.jsonl        one row per pair: case_id, task, structure, modality, timepoint,
                   image, mask, shape, spacing_mm  (single split; no official split exists)

Licensing

• Images (RESECT, NIRD archive, DOI 10.11582/2017.00004): CC BY 4.0
• Masks (RESECT-SEG, osf.io/jv8bk): CC BY-NC-SA 4.0 — "gaining any financial benefits from the distribution of the proposed annotation dataset is prohibited"
• Combined repo therefore carries CC BY-NC-SA 4.0 (the more restrictive component).

Benchmark contamination warning

These 23 patients ARE the training data of CuRIOUS 2018/2019/2022 and (as the resampled 22-case EASY-RESECT variant) of Learn2Reg 2020. Any model trained on those challenge releases has seen these cases; cross-reference by case_id. The challenges' private test cases (10 in 2018/19, 6 in 2022) were never publicly released. No patient overlap with BITE, ReMIND, BraTS, MSD, or TCIA collections. Note: EASY-RESECT's *-seg.nii.gz files are voxelized landmark spheres, NOT anatomy — they are unrelated to these masks and are not included here.

Citation

Please cite both:

1. Xiao Y, Fortin M, Unsgard G, Rivaz H, Reinertsen I. REtroSpective Evaluation of Cerebral Tumors (RESECT): A clinical database of pre-operative MRI and intra-operative ultrasound in low-grade glioma surgeries. Medical Physics 2017;44(7):3875-3882. doi:10.1002/mp.12268
2. Behboodi B, Carton FX, Chabanas M, De Ribaupierre S, Solheim O, Munkvold BKR, Rivaz H, Xiao Y, Reinertsen I. Open access annotations of intra-operative brain tumor ultrasound images. Medical Physics 2024;51(9):6525-6532. doi:10.1002/mp.17317