Deep learning for DSI parameter map generation without image pre-processing
Eric Kenneth Gibbons1, Kyler K. Hodgson2, Ganesh Adluru1, and Edward VR DiBella1

1Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT, United States, 2Bioengineering, University of Utah, Salt Lake City, UT, United States


Recent advances in diffusion spectrum imaging (DSI) have reduced scan time considerably. Through the use of deep learning, DSI parameter maps (NODDI, GFA, etc.) can be generated with only a fraction of the number of q-space samples compared to conventional acquisition strategies. However, image pre-processing prior to the deep learning parameter map generation step is a computational bottleneck. This abstract explores if this bottleneck can be bypassed entirely and use images straight from the scanner as CNN inputs. We show that the image pre-processing is not necessary to generate NODDI and GFA parameter maps--thereby avoiding the image processing computation time.


Diffusion magnetic resonance imaging (MRI) is an invaluable tool in neuroimaging and is included in many neurological protocols for imaging intracranial diseases such as stroke, infection, and tumor monitoring. Common quantitative diffusion imaging techniques include diffusion tensor imaging (DTI) and diffusion spectrum imaging (DSI). DSI techniques--particularly quantitative approaches such as generalized fractional anisotropy (GFA)--aim to generalize DTI by increased sampling of q-space, though at the cost of increased scan time. While advances have reduced DSI scan time to 15 minutes, DTI still remains the clinical standard. Recent Deep learning techniques have further reduced DSI imaging scan time to the order of 2-3 minutes[1,2].

Deep learning techniques have relied on extensive image pre-processing prior to being fed into the neural network. This pipeline consists of for example skull stripping[3], noise removal[4], removal of noise bias[5], Gibb’s ringing correction[6], and off-resonance and eddy current distortion removal. While the network has been demonstrated to achieve high performance with these preprocessed images, using this pipeline is cumbersome. In particular, a scan with 51 slices can take up to two hours to process, which can hamper clinical feasibility. This work examines the necessity of using these pre-processing techniques or if deep learning networks can be successful given noisy inputs with no pre-processing.


DSI data were acquired from 48 scans from a total of 29 subjects. All DSI data were acquired using a Siemens 3T Verio (Erlangen, Germany) with max gradient strength of 45 mT/m, maximum slew rate of 200 mT/m/s, and a 32 channel head coil. Each DSI scan acquired data with a maximum b-value of 4000 s/mm2 and 203 directions. For all scans, a simultaneous multi-slice blipped CAIPIRINHA pulse sequence with a threefold slice acceleration was used to acquire 51 slices per participant. The field-of-view was 250 mm x 250 mm with a voxel dimension of 1.9 mm x 1.9 mm x 2.1 mm. The TE/TR was 114.2 ms / 3.7 s. The total data acquisition time for each DSI scan was approximately 13 minutes.

The data were pre-processed using the pipeline described above. A neural network as in [2] (see Fig. 1) was trained using the unprocessed and pre-processed data separately. Fig. 2 shows an example of both the pre-processed and the unprocessed data. Additionally, a deeper network (the same basic architecture as in [2] but with twice the number of layers) was trained using the unprocessed data to determine if there could be performance gains by modifying the network architecture. Comparisons for ODI and GFA against a reference were done by comparing standard metrics: NRMSE, PSNR, SSIM.


Fig. 3 shows example output images where q-space was subsampled to only 24 directions for three scenarios: the original network and preprocessed input data, the original network and unprocessed data, and a deeper network with unprocessed data. In difference images, eddy current correction is not resolved by the neural networks showing strong deviations from the reference along the perimeter of the brain.

Quantitative results are seen in Fig. 4. It is clear from the box and whisker plots that the preprocessed data result in higher fidelity output images in terms of SSIM, PSNR, and NRMSE. Additionally, the shallower network also outperforms the deeper network across all metrics.


While the preprocessed input provides higher fidelity output images based on standard quantitative image comparison metrics, it is misguided to discount the method of using the unprocessed images. Much of superiority of the pre-processed case in terms of quantitative metrics seen in Fig. 4 likely comes from image blurring for the outputs for the unprocessed images as well as failure to correct for eddy current-induced image warping. In terms of blurring, we hypothesize that because the input images are inherently noisy, the network learns considerable noise suppression, which leads to image blurring as a secondary effect. This seems compounded in the case of the deeper network where there are more convolutional layers, which is likely why we see more blurring in those images compared to the shallower network. In terms of image warping, the edges of the output images will not perfectly align with the edges of the reference images. While the network is able to resolve parameter maps through noise, noise bias, and Gibb’s ringing, it may not fully handle image distortion. There is some improvement in this area by using a deeper network.


We have demonstrated a rapid method of generating DSI parameter maps using unprocessed images as inputs to a convolutional neural network with slight compromise in image fidelity. Future improvements could include a separate network to handle the image pre-processing steps to achieve both higher parameter map fidelity as well as processing speed.


The authors would like to thank the Departments of Neurology and Occupational and Recreational Therapies for assistance in data collection.


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Fig. 1: Example comparisons between images with and without image processing.

Fig. 2: Basic network architecture used for NODDI/GFA processing. A deeper version of this network is also used where the number of residual blocks is doubled.

Fig. 3: An example slice is presented using the standard CNN architecture using preprocessed input data, the standard CNN architecture using unprocessed input data, and a deeper architecture using unprocessed input data. Each sub-sampled image is accompanied with an absolute difference image, which is found against the reference standard. In this case, we treat the parameter images derived from fully sampled q-space as the ground truth reference standard.

Fig. 4: Image quality metric comparisons for the CNN using pre-processed inputs, the CNN using unprocessed inputs, and a deeper CNN using unprocessed inputs against a ground truth reference standard. Each column corresponds to a different parameter map (ODI and GFA). Each row corresponds to a different image quality metric (SSIM, PSNR, and NRMS). Data points are from different numbers of diffusion directions used in the parameter map reconstruction. This figure suggests that pre-processing lead to higher image fidelity. Between the two depths of CNN architecture, the shallower network appears to outperform the deeper network.

Proc. Intl. Soc. Mag. Reson. Med. 27 (2019)