Simultaneous Segmentation and Relaxometry for MRI through Multitask Learning (1911.12389v1)

Abstract: Purpose: This study demonstrated an MR signal multitask learning method for 3D simultaneous segmentation and relaxometry of human brain tissues. Materials and Methods: A 3D inversion-prepared balanced steady-state free precession sequence was used for acquiring in vivo multi-contrast brain images. The deep neural network contained 3 residual blocks, and each block had 8 fully connected layers with sigmoid activation, layer norm, and 256 neurons in each layer. Online synthesized MR signal evolutions and labels were used to train the neural network batch-by-batch. Empirically defined ranges of T1 and T2 values for the normal gray matter, white matter and cerebrospinal fluid (CSF) were used as the prior knowledge. MRI brain experiments were performed on 3 healthy volunteers as well as animal (N=6) and prostate patient (N=1) experiments. Results: In animal validation experiment, the differences/errors (mean difference $\pm$ standard deviation of difference) between the T1 and T2 values estimated from the proposed method and the ground truth were 113 $\pm$ 486 and 154 $\pm$ 512 ms for T1, and 5 $\pm$ 33 and 7 $\pm$ 41 ms for T2, respectively. In healthy volunteer experiments (N=3), whole brain segmentation and relaxometry were finished within ~5 seconds. The estimated apparent T1 and T2 maps were in accordance with known brain anatomy, and not affected by coil sensitivity variation. Gray matter, white matter, and CSF were successfully segmented. The deep neural network can also generate synthetic T1 and T2 weighted images. Conclusion: The proposed multitask learning method can directly generate brain apparent T1 and T2 maps, as well as synthetic T1 and T2 weighted images, in conjunction with segmentation of gray matter, white matter and CSF.