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Deep learning enables automatic detection and segmentation of brain metastases on multisequence MRI

Publication Type:

Journal Article


J Magn Reson Imaging, Volume 51, Number 1, p.175-182 (2020)


1522-2586 (Electronic)<br/>1053-1807 (Linking)

Accession Number:




*brain metastases, *Deep Learning, *multisequence, *segmentation


BACKGROUND: Detecting and segmenting brain metastases is a tedious and time-consuming task for many radiologists, particularly with the growing use of multisequence 3D imaging. PURPOSE: To demonstrate automated detection and segmentation of brain metastases on multisequence MRI using a deep-learning approach based on a fully convolution neural network (CNN). STUDY TYPE: Retrospective. POPULATION: In all, 156 patients with brain metastases from several primary cancers were included. FIELD STRENGTH: 1.5T and 3T. [Correction added on May 24, 2019, after first online publication: In the preceding sentence, the first field strength listed was corrected.] SEQUENCE: Pretherapy MR images included pre- and postgadolinium T1 -weighted 3D fast spin echo (CUBE), postgadolinium T1 -weighted 3D axial IR-prepped FSPGR (BRAVO), and 3D CUBE fluid attenuated inversion recovery (FLAIR). ASSESSMENT: The ground truth was established by manual delineation by two experienced neuroradiologists. CNN training/development was performed using 100 and 5 patients, respectively, with a 2.5D network based on a GoogLeNet architecture. The results were evaluated in 51 patients, equally separated into those with few (1-3), multiple (4-10), and many (>10) lesions. STATISTICAL TESTS: Network performance was evaluated using precision, recall, Dice/F1 score, and receiver operating characteristic (ROC) curve statistics. For an optimal probability threshold, detection and segmentation performance was assessed on a per-metastasis basis. The Wilcoxon rank sum test was used to test the differences between patient subgroups. RESULTS: The area under the ROC curve (AUC), averaged across all patients, was 0.98 +/- 0.04. The AUC in the subgroups was 0.99 +/- 0.01, 0.97 +/- 0.05, and 0.97 +/- 0.03 for patients having 1-3, 4-10, and >10 metastases, respectively. Using an average optimal probability threshold determined by the development set, precision, recall, and Dice score were 0.79 +/- 0.20, 0.53 +/- 0.22, and 0.79 +/- 0.12, respectively. At the same probability threshold, the network showed an average false-positive rate of 8.3/patient (no lesion-size limit) and 3.4/patient (10 mm(3) lesion size limit). DATA CONCLUSION: A deep-learning approach using multisequence MRI can automatically detect and segment brain metastases with high accuracy. LEVEL OF EVIDENCE: 3 Technical Efficacy Stage: 2 J. Magn. Reson. Imaging 2020;51:175-182.