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UCSD-PTGBM – Post-Treatment High-Grade Glioma Multimodal MRI Dataset

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@data-hcp data-hcp released this 28 Mar 03:55
ucsd-ptgbm
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This dataset provides a large-scale, post-operative glioblastoma MRI cohort with advanced imaging modalities, expert annotations, and clinical outcomes, designed to support research in tumor progression, treatment response, and radiogenomics.

Dataset Overview

  • Subjects: 178 patients

  • Timepoints: 243 imaging sessions

  • Cancer type: High-grade glioma (glioblastoma)

  • Mean age: 56 ± 13 years

  • Sex: 116 male, 62 female

  • Total size: ~44.98 GB :contentReference[oaicite:0]{index=0}

  • Scanner: 3T clinical MRI (GE systems)

Imaging Modalities

Structural MRI

  • Pre- and post-contrast T1-weighted (3D IR-SPGR)
  • T2-weighted FLAIR

Diffusion MRI (Multishell RSI)

  • b-values: 0, 500, 1500, 4000 s/mm²
  • Multi-direction acquisition
  • Enables cellularity mapping via Restricted Spectrum Imaging (RSI)

Perfusion Imaging

  • DSC (Dynamic Susceptibility Contrast)
  • ASL (Arterial Spin Labeling)

Key Features

  • Post-operative dataset (rare compared to pre-op datasets)

  • Multishell diffusion MRI for separating:

    • Tumor cellularity
    • Edema / free water

  • Expert-validated tumor segmentation

    • Based on BraTS standards
    • Manually refined by neuroradiologists

  • Cellular tumor annotations

    • Enhancing tumor (ECT)
    • Non-enhancing tumor (NECT)
    • Total cellular tumor (TCT)

  • Clinical and molecular data

    • IDH mutation status
    • MGMT promoter methylation
    • Overall survival (OS)
    • Progression-free survival (PFS)

Dataset Composition

Imaging Data

  • Multimodal MRI (NIfTI format)
  • Co-registered to 1 mm isotropic MNI space

Segmentations

  • Multi-compartment tumor labels
  • Radiologist-approved voxelwise annotations

Clinical Data

  • Demographics
  • Diagnosis and treatment
  • Follow-up outcomes

Additional Files

  • b-values / b-vectors
  • Negative case categorization

Cohort Details

  • Residual or recurrent tumor: 192 timepoints

  • Post-treatment changes only: 51 timepoints

    • Includes:
      • Pseudoprogression
      • Radiation necrosis
      • Non-specific treatment effects

  • Survival data available: subset of 94 patients

Preprocessing

  • RSI cellularity modeling via linear mixture modeling
  • Beam-forming filter for signal refinement
  • DSC processed with leakage-corrected CBV
  • Skull stripping via nnUNet-based pipeline
  • All modalities registered to MNI space

Scientific Applications

  • Post-treatment tumor assessment
  • Differentiation of recurrence vs treatment effects
  • Radiogenomics and biomarker discovery
  • AI/ML for segmentation and prognosis
  • Diffusion-based tumor microstructure modeling

License

  • Creative Commons Attribution 4.0 (CC BY 4.0)

Citation

Gagnon et al., 2025
The UCSD-PTGBM dataset (Version 3)
https://doi.org/10.7937/fwv2-dt74

Notes

  • One of the few publicly available post-operative glioma datasets
  • Includes advanced diffusion + perfusion imaging, uncommon in open datasets
  • Particularly valuable for clinical translation and longitudinal analysis

participants.tsv Fields

The participants.tsv file includes scanner, demographic, diagnostic, molecular, treatment, and outcome variables for each case.

Data Collection Name Data Descriptor / Metadata Name
ID TCIA ID
Brats Subject ID ID used in the BraTS 2024 challenge
Magnetic Field Strength Magnetic field strength of the scanner
Manufacturer Manufacturer of the scanner
Manufacturer's Model Name Model name of the scanner
Patient's Age At time of scan (in years)
Sex at birth M/F
Race American Indian or Alaska Native / Asian / Native Hawaiian or Pacific Islander / Black or African American / White / Unknown / Not Reported
Ethnicity Hispanic or Latino / Not Hispanic or Latino / Unknown / Not Reported
Primary Diagnosis Glioblastoma; Oligoastrocytoma; Astrocytoma, IDH-Mutant, Grade 4; Anaplastic Astrocytoma
Days from Acquisition to Date of initial surgery, treatment or diagnosis Either date of surgery, or other initial treatment if the patient did not undergo surgery at the time of diagnosis, or date of diagnosis if the patient did not receive any treatment
Days from Acquisition to Date of last surgery prior to scan if different Date of last surgery prior to scan if different from the date of initial surgery
WHO 2021 Diagnosis Diagnostic classification according to WHO 2021 criteria
Non WHO 2021 Diagnosis Diagnostic classification prior to WHO 2021
Grade Grade according to criteria at the time of diagnosis
MGMT MGMT methylation status, either methylated or unmethylated
IDH IDH mutation status, either mutated or wild type
1p19q 1p19q codeletion status, either codeleted or intact (= not 1p19q codeleted)
ATRX ATRX status. Loss = indication of mutation; intact = ATRX retained, no indication of mutation
Days from Acquisition to Date of last follow-up Date of last follow-up from the clinical record
Days from Acquisition to Date of death Date of death
Overall survival Days between initial surgery and death
Progression free survival Days between initial surgery and first sign of progression
Surgery Yes/No
Number of surgeries Number of surgeries
Surgery extend GTR / STR / Biopsy
Radiation Yes/No
Number of radiation courses Number of radiation courses
Days from Acquisition to Date of first radiation Date of first radiation
Days from Acquisition to Date of last radiation prior to scan Date of last radiation prior to scan
1st Chemo type Type of first chemotherapy agent
Days from Acquisition to Date of 1st chemo start Date of first chemotherapy treatment start
Avastin® (bevacizumab) Yes/No
Days from Acquisition to Date of last Avastin treatment prior to scan Date of last Avastin treatment prior to scan
Other treatment prior to scan Yes/No
Days from Acquisition to Other treatment dates Date of other treatment if known
Assets 1,002
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