Fast learning of fiber orientation distribution function for MR tractography using convolutional neural network
Authors: Lin Zhichao , Gong Ting , Wang Kewen , Li Zhiwei , He Hongjian , Tong Qiqi , Yu Feng , Zhong Jianhui 
Published: April 2019

Purpose

In diffusion‐weighted magnetic resonance imaging (DW‐MRI), the fiber orientation distribution function (fODF) is of great importance for solving complex fiber configurations to achieve reliable tractography throughout the brain, which ultimately facilitates the understanding of brain connectivity and exploration of neurological dysfunction. Recently, multi‐shell multi‐tissue constrained spherical deconvolution (MSMT‐CSD) method has been explored for reconstructing full fODFs. To achieve a reliable fitting, similar to other model‐based approaches, a large number of diffusion measurements is typically required for MSMT‐CSD method. The prolonged acquisition is, however, not feasible in practical clinical routine and is prone to motion artifacts. To accelerate the acquisition, we proposed a method to reconstruct the fODF from downsampled diffusion‐weighted images (DWIs) by leveraging the strong inference ability of the deep convolutional neural network (CNN).

Methods

The method treats spherical harmonics (SH)‐represented DWI signals and fODF coefficients as inputs and outputs, respectively. To compensate for the reduced gradient directions with reduced number of DWIs in acquisition in each voxel, its surrounding voxels are incorporated by the network for exploiting their spatial continuity. The resulting fODF coefficients are fitted with applying the CNN in a multi‐target regression model. The network is composed of two convolutional layers and three fully connected layers. To obtain an initial evaluation of the method, we quantitatively measured its performance on a simulated dataset. Then, for in vivo tests, we employed data from 24 subjects from the Human Connectome Project (HCP) as training set and six subjects as test set. The performance of the proposed method was primarily compared to the super‐resolved MSMT‐CSD with the decreasing number of DWIs. The fODFs reconstructed by MSMT‐CSD from all available 288 DWIs were used as training labels and the reference standard. The performance was quantitatively measured by the angular correlation coefficient (ACC) and the mean angular error (MAE).

Results

For the simulated dataset, the proposed method exhibited the potential advantage over the model reconstruction. For the in vivo dataset, it achieved superior results over the MSMT‐CSD in all the investigated cases, with its advantage more obvious when a limited number of DWIs were used. As the number of DWIs was reduced from 95 to 25, the median ACC ranged from 0.96 to 0.91 for the CNN, but 0.93 to 0.77 for the MSMT‐CSD (with perfect score of 1). The angular error in the typical regions of interest (ROIs) was also much lower, especially in multi‐fiber regions. The average MAE for the CNN method in regions containing one, two, three fibers was, respectively, 1.09°, 2.75°, and 8.35° smaller than the MSMT‐CSD method. The visual inception of the fODF further confirmed this superiority. Moreover, the tractography results validated the effectiveness of the learned fODF, in preserving known major branching fibers with only 25 DWIs.

Conclusion

Experiments on HCP datasets demonstrated the feasibility of the proposed method in recovering fODFs from up to 11‐fold reduced number of DWIs. The proposed method offers a new streamlined reconstruction procedure and exhibits promising potential in acquisition acceleration for the reconstruction of fODFs with good accuracy.