QuickNAT: Segmenting MRI Neuroanatomy in 20 seconds

Whole brain segmentation from structural magnetic resonance imaging is a prerequisite for most morphological analyses, but requires hours of processing time and therefore delays the availability of image markers after scan acquisition. We introduce QuickNAT, a fully convolution neural network that segments a brain scan in 20 seconds. To enable training of the complex network with limited annotated data, we propose to pre-train on auxiliary labels created from existing segmentation software and to subsequently fine-tune on manual labels. In an extensive set of evaluations on eight datasets that cover a wide age range, pathology, and different scanners, we demonstrate that QuickNAT achieves superior performance to state-of-the-art methods, while being about 700 times faster. This drastic speed up greatly facilitates the processing of large data repositories and supports the translation of imaging biomarkers by making them almost instantaneously available.