TCIA TCGA-GBM MRI Collection

Overview

The TCIA TCGA-GBM collection provides pre-operative multi-parametric MRI scans for 135 glioblastoma multiforme (GB) patients drawn from the TCGA-GBM cohort (originating set n=262 from 8 institutions). Bakas et al. 2017 released expert-revised tumour segmentation labels (whole tumour, tumour core, enhancing tumour) and >700 extracted radiomic features for these cases. The molecular and genomic counterpart is the cBioPortal study gbm_tcga. PMID:28872634

Composition

  • Cancer type: glioblastoma multiforme (GB), n=135 (from originating set of 262).
  • Modality: multi-parametric MRI — T1, T1-Gd (post-contrast), T2, T2-FLAIR; retrospective standard-of-care acquisitions from GE, Siemens, Philips, and Hitachi scanners at field strengths 0.5–3 T.
  • Pre-processing: re-orientation to LPS, affine co-registration to T1 template via FSL FLIRT, resampling to 1 mm³, skull-stripping with BET, SUSAN smoothing.
  • Annotations: expert-revised segmentation labels generated using GLISTRboost then manually corrected; labels cover whole tumour (WT), tumour core (TC), and enhancing tumour (ET) sub-regions. PMID:28872634

Assays / panels (linked)

Papers using this cohort

  • PMID:28872634 — Bakas et al. 2017, Scientific Data: primary data resource paper; releases expert-revised MRI segmentation labels and >700 radiomic features for 135 TCGA-GBM cases; labels became the BraTS’17 reference standard.

Notable findings derived from this cohort

  • Expert-revised labels vs. GLISTRboost automated labels: median DICE 0.92 (WT), 0.88 (TC), 0.88 (ET); median Jaccard 0.96 (WT), 0.87 (TC), 0.86 (ET) — manual revision most impacted core/enhancing sub-regions. PMID:28872634
  • 95th-percentile Hausdorff distances: 3.61 mm (WT), 4.06 mm (TC), 2.00 mm (ET). PMID:28872634
  • N=200 GBM cases overlap with BraTS’15 training set; N=23 with BraTS’15 testing set. The revised labels became the BraTS’17 reference standard. PMID:28872634

Sources

  • TCIA collection: TCGA-GBM — https://www.cancerimagingarchive.net/collection/tcga-gbm/
  • cBioPortal genomic counterpart: gbm_tcga
  • PMID:28872634 — Bakas et al. 2017, Scientific Data, DOI 10.1038/sdata.2017.117.

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