Real-Time Automatic Fetal Brain Extraction in Fetal MRI by Deep Learning

• Main Authors: Salehi, Seyed Sadegh Mohseni, Hashemi, Seyed Raein, Velasco-Annis, Clemente, Ouaalam, Abdelhakim, Estroff, Judy A, Erdogmus, Deniz, Warfield, Simon K, Gholipour, Ali
• Format: Journal Article
• Language: English
• Published: 25-10-2017
• Subjects: Computer Science - Computer Vision and Pattern Recognition
• DOI: 10.48550/arxiv.1710.09338

Brain segmentation is a fundamental first step in neuroimage analysis. In the
case of fetal MRI, it is particularly challenging and important due to the
arbitrary orientation of the fetus, organs that surround the fetal head, and
intermittent fetal motion. Several promising methods have been proposed but are
limited in their performance in challenging cases and in real-time
segmentation. We aimed to develop a fully automatic segmentation method that
independently segments sections of the fetal brain in 2D fetal MRI slices in
real-time. To this end, we developed and evaluated a deep fully convolutional
neural network based on 2D U-net and autocontext, and compared it to two
alternative fast methods based on 1) a voxelwise fully convolutional network
and 2) a method based on SIFT features, random forest and conditional random
field. We trained the networks with manual brain masks on 250 stacks of
training images, and tested on 17 stacks of normal fetal brain images as well
as 18 stacks of extremely challenging cases based on extreme motion, noise, and
severely abnormal brain shape. Experimental results show that our U-net
approach outperformed the other methods and achieved average Dice metrics of
96.52% and 78.83% in the normal and challenging test sets, respectively. With
an unprecedented performance and a test run time of about 1 second, our network
can be used to segment the fetal brain in real-time while fetal MRI slices are
being acquired. This can enable real-time motion tracking, motion detection,
and 3D reconstruction of fetal brain MRI.