Glioma Brain Tumor Segmentation

For the PICTURE data, 275 GBM and 205 LGG cases were manually segmented into 3 classes consistent with the BraTS challenges – whole tumor (WT), tumor core (TC), and enhancing tumor (ET), see Fig. 1. The WT defines the full extent of the tumor, including the tumor core and oedema, indicated by hyperintensity on FLAIR and T2w. The TC is the main body of the tumor and most likely area of resection. The TC includes the enhancing tumor (ET) and necrosis.
Manual segmentations were carried out according to the VASARI Research Project (https://wiki.cancerimagingarchive.net/display/Public/VASARI+Research+Project). One rater (HP) with 9 years of brain MRI manual segmentation experience performed segmentations under the supervision and approval of an expert neuroradiologist (FB), using the semiautomatic SmartBrush tool (BrainLab, Feldkirchen, Germany). The rater’s performance was in line with experts^{29 (link)}. All segmentations were exported on the T1c image. The segmentation was resampled to SRI24 atlas space using the same transform from the T1c to SRI24 registration.

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Pemberton H.G., Wu J., Kommers I., Müller D.M., Hu Y., Goodkin O., Vos S.B., Bisdas S., Robe P.A., Ardon H., Bello L., Rossi M., Sciortino T., Nibali M.C., Berger M.S., Hervey-Jumper S.L., Bouwknegt W., Van den Brink W.A., Furtner J., Han S.J., Idema A.J., Kiesel B., Widhalm G., Kloet A., Wagemakers M., Zwinderman A.H., Krieg S.M., Mandonnet E., Prados F., de Witt Hamer P., Barkhof F, & Eijgelaar R.S. (2023). Multi-class glioma segmentation on real-world data with missing MRI sequences: comparison of three deep learning algorithms. Scientific Reports, 13, 18911.

Publication 2023

SmartBrush tool

Body Brain Necrosis Oedema Supervision Tumor

Corresponding Organization :

Other organizations : University College London, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, National Hospital for Neurology and Neurosurgery, University Medical Center Utrecht, Elisabeth-TweeSteden Ziekenhuis, University of Milan, University of California, San Francisco, Neurological Surgery, Isala, Medical University of Vienna, Stanford University, Medisch Centrum Haaglanden, University Medical Center Groningen, University of Groningen, Academic Medical Center, Klinikum rechts der Isar, Technical University of Munich, Hôpital Lariboisière, Assistance Publique – Hôpitaux de Paris, Amsterdam UMC Location VUmc

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Variable analysis

independent variables

Manual segmentation of cases into 3 classes: whole tumor (WT), tumor core (TC), and enhancing tumor (ET)

dependent variables

Performance of the rater (HP) with 9 years of brain MRI manual segmentation experience

control variables

Segmentations were performed under the supervision and approval of an expert neuroradiologist (FB)
Rater's performance was in line with experts

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