fidopt Interactive view
Lesions and tumours, segmentation

ReMIND, brain tumour before resection

Pre-operative head MR of an adult about to have a brain tumour resected at Brigham and Women's Hospital: the one defaced series the surgical team outlined the tumour on, with that whole-tumour outline (ReMIND, TCIA).

10 test casesbrainimage MR
Look at the images
Read before comparing (12)
  • Cohort. 114 consecutive patients operated on with image guidance: gliomas, 11 metastases and other lesions, a few found by pathology not to be tumours. 51 had a craniotomy before, 43 of the 97 in the pool.
  • Cases. The series the outline names: a contrast-enhanced T1 for 54 pool patients, a T2 for 27, a FLAIR for 12 and a T1 without contrast for 4, the draw's strata. The test cases are six contrast-enhanced T1, three T2 SPACE and one 2D FLAIR. A method is told mr, not the contrast.
  • One series. The provider gives no patient's sequences on one grid, and only 7 of the 114 have all four before surgery: the dataset joins the single-image lesion sets, not the brain tumour track.
  • Images. The DICOM series as TCIA serves them, values untouched, defaced by the provider, skull and scalp kept; no mask. Nine test cases are 3D at about 1 mm; ReMIND-111 is a 2D FLAIR of 55 slices 3 mm apart. On all 20 cases the outline lies on the side the clinical spreadsheet gives.
  • Outline grid. On 8 of the 20 cases (test cases ReMIND-014, 070, 072, 086 and 111, development cases 010, 027 and 100) the provider's outline lies on another lattice; prepare.py brings it onto the image's grid by nearest neighbour in world coordinates, its edge within half a voxel.
  • Truth. For surgical planning a neurosurgical fellow outlined the tumour by hand and the attending neurosurgeon refined it if needed: the enhancing region with any necrotic core, or the solid part within the T2 and FLAIR hyperintensity, without oedema. It is a surgeon's target: on ReMIND-106 it follows straight lines, and on non-enhancing tumours its edge is a judgement.
  • Agreement. Two neurosurgical research fellows outlined ten cases again: a Dice of 0.922 (SD 0.028) and a mean surface distance of 0.68 mm on five enhancing tumours, 0.864 (SD 0.037) and 1.24 mm on five non-enhancing ones.
  • Room. A test outline moved by one voxel keeps a Dice of 0.89 to 0.96: above about 0.9 methods differ within the truth's spread. The surface Dice, at 1 mm, is stricter than the observers on non-enhancing tumours.
  • Name. The label, brain_tumour, is close to BraTS's tumour core for enhancing tumours and to the whole tumour for the others. Outlines of cavities, residual tumour and targets, and Brainlab's automatic structures, are left out.
  • Tumours. The ten test outlines hold 4.5 to 69.3 ml (median 24.3), each in one piece, among them a metastasis (ReMIND-014) and treatment effects (072). Four were operated on before (049, 070, 075 and 106), so an older cavity lies beside the outline.
  • Outside numbers. None is scored as here. The outlines are public: a network trained on ReMIND may have seen these patients.
  • Overlap. No other dataset of the corpus holds these patients. Learn2Reg's ReMIND2Reg and the screening's ReMIND rows hold the same patients: a dataset built later from them keeps these test patients in its test cases and these development patients out of them.

No method has a result on every case of this dataset yet.

Case by case

Click a score to look at that result: the image, the truth in green and the method's map in red. Underlined scores have their image; for the others you see the case without the result.

About the data

The first test case of ReMIND, brain tumour before resection
The first test caseClick to look at every case.
Test cases
10 test patients drawn with seed 2026 by the contrast of the outlined series among the 87 outside development; 10 development patients, the last of the same seeded order, each contrast in proportion (six contrast-enhanced T1, three T2, one FLAIR). The pool is the 97 of 114 patients with one pre-operative outline: 16 have two, ReMIND-032 none.
Truth
contours by experts the dataset's pre-operative whole tumour, outlined by hand for surgical planning in Brainlab Elements by a neurosurgical fellow and refined where needed by the attending neurosurgeon: the enhancing region with any necrotic core for an enhancing tumour, the solid or nodular part within the T2 and FLAIR hyperintensity for one that does not enhance
Licence
CC BY 4.0
10 cases for tuning, never tested

ReMIND-050, ReMIND-054, ReMIND-013, ReMIND-094, ReMIND-029, ReMIND-027, ReMIND-105, ReMIND-112, ReMIND-100, ReMIND-010