Generating Diffusion MRI scalar maps from T1 weighted images using generative adversarial networks

Diffusion magnetic resonance imaging (diffusion MRI) is a non-invasive microstructure assessment technique. Scalar measures, such as FA (fractional anisotropy) and MD (mean diffusivity), quantifying micro-structural tissue properties can be obtained using diffusion models and data processing pipelines. However, it is costly and time consuming to collect high quality diffusion data. Here, we therefore demonstrate how Generative Adversarial Networks (GANs) can be used to generate synthetic diffusion scalar measures from structural T1-weighted images in a single optimized step. Specifically, we train the popular CycleGAN model to learn to map a T1 image to FA or MD, and vice versa. As an application, we show that synthetic FA images can be used as a target for non-linear registration, to correct for geometric distortions common in diffusion MRI

Optic Flow Stimuli in and Near the Visual Field Centre: A Group fMRI Study of Motion Sensitive Regions

Motion stimuli in one visual hemifield activate human primary visual areas of the contralateral side, but suppress activity of the corresponding ipsilateral regions. While hemifield motion is rare in everyday life, motion in both hemifields occurs regularly whenever we move. Consequently, during motion primary visual regions should simultaneously receive excitatory and inhibitory inputs. A comparison of primary and higher visual cortex activations induced by bilateral and unilateral motion stimuli is missing up to now. Many motion studies focused on the MT+ complex in the parieto-occipito-temporal cortex. In single human subjects MT+ has been subdivided in area MT, which was activated by motion stimuli in the contralateral visual field, and area MST, which responded to motion in both the contra- and ipsilateral field. In this study we investigated the cortical activation when excitatory and inhibitory inputs interfere with each other in primary visual regions and we present for the first time group results of the MT+ subregions, allowing for comparisons with the group results of other motion processing studies. Using functional magnetic resonance imaging (fMRI), we investigated whole brain activations in a large group of healthy humans by applying optic flow stimuli in and near the visual field centre and performed a second level analysis. Primary visual areas were activated exclusively by motion in the contralateral field but to our surprise not by central flow fields. Inhibitory inputs to primary visual regions appear to cancel simultaneously occurring excitatory inputs during central flow field stimulation. Within MT+ we identified two subregions. Putative area MST (pMST) was activated by ipsi- and contralateral stimulation and located in the anterior part of MT+. The second subregion was located in the more posterior part of MT+ (putative area MT, pMT)

A Conceptual Cortical Surface Atlas

Volumetric, slice-based, 3-D atlases are invaluable tools for understanding complex cortical convolutions. We present a simple scheme to convert a slice-based atlas to a conceptual surface atlas that is easier to visualize and understand. The key idea is to unfold each slice into a one-dimensional vector, and concatenate a succession of these vectors – while maintaining as much spatial contiguity as possible – into a 2-D matrix. We illustrate our methodology using a coronal slice-based atlas of the Rhesus Monkey cortex. The conceptual surface-based atlases provide a useful complement to slice-based atlases for the purposes of indexing and browsing

Learning-based Ensemble Average Propagator Estimation

By capturing the anisotropic water diffusion in tissue, diffusion magnetic resonance imaging (dMRI) provides a unique tool for noninvasively probing the tissue microstructure and orientation in the human brain. The diffusion profile can be described by the ensemble average propagator (EAP), which is inferred from observed diffusion signals. However, accurate EAP estimation using the number of diffusion gradients that is clinically practical can be challenging. In this work, we propose a deep learning algorithm for EAP estimation, which is named learning-based ensemble average propagator estimation (LEAPE). The EAP is commonly represented by a basis and its associated coefficients, and here we choose the SHORE basis and design a deep network to estimate the coefficients. The network comprises two cascaded components. The first component is a multiple layer perceptron (MLP) that simultaneously predicts the unknown coefficients. However, typical training loss functions, such as mean squared errors, may not properly represent the geometry of the possibly non-Euclidean space of the coefficients, which in particular causes problems for the extraction of directional information from the EAP. Therefore, to regularize the training, in the second component we compute an auxiliary output of approximated fiber orientation (FO) errors with the aid of a second MLP that is trained separately. We performed experiments using dMRI data that resemble clinically achievable $q$-space sampling, and observed promising results compared with the conventional EAP estimation method.Comment: Accepted by MICCAI 201

Modelling the Distribution of 3D Brain MRI using a 2D Slice VAE

Probabilistic modelling has been an essential tool in medical image analysis, especially for analyzing brain Magnetic Resonance Images (MRI). Recent deep learning techniques for estimating high-dimensional distributions, in particular Variational Autoencoders (VAEs), opened up new avenues for probabilistic modeling. Modelling of volumetric data has remained a challenge, however, because constraints on available computation and training data make it difficult effectively leverage VAEs, which are well-developed for 2D images. We propose a method to model 3D MR brain volumes distribution by combining a 2D slice VAE with a Gaussian model that captures the relationships between slices. We do so by estimating the sample mean and covariance in the latent space of the 2D model over the slice direction. This combined model lets us sample new coherent stacks of latent variables to decode into slices of a volume. We also introduce a novel evaluation method for generated volumes that quantifies how well their segmentations match those of true brain anatomy. We demonstrate that our proposed model is competitive in generating high quality volumes at high resolutions according to both traditional metrics and our proposed evaluation.Comment: accepted for publication at MICCAI 2020. Code available https://github.com/voanna/slices-to-3d-brain-vae

Diffusion Tensor Model links to Neurite Orientation Dispersion and Density Imaging at high b-value in Cerebral Cortical Gray Matter

Diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) are widely used models to infer microstructural features in the brain from diffusion-weighted MRI. Several studies have recently applied both models to increase sensitivity to biological changes, however, it remains uncertain how these measures are associated. Here we show that cortical distributions of DTI and NODDI are associated depending on the choice of b-value, a factor reflecting strength of diffusion weighting gradient. We analyzed a combination of high, intermediate and low b-value data of multi-shell diffusion-weighted MRI (dMRI) in healthy 456 subjects of the Human Connectome Project using NODDI, DTI and a mathematical conversion from DTI to NODDI. Cortical distributions of DTI and DTI-derived NODDI metrics were remarkably associated with those in NODDI, particularly when applied highly diffusion-weighted data (b-value = 3000 sec/mm^{2}). This was supported by simulation analysis, which revealed that DTI-derived parameters with lower b-value datasets suffered from errors due to heterogeneity of cerebrospinal fluid fraction and partial volume. These findings suggest that high b-value DTI redundantly parallels with NODDI-based cortical neurite measures, but the conventional low b-value DTI is hard to reasonably characterize cortical microarchitecture

Whole MILC: generalizing learned dynamics across tasks, datasets, and populations

Behavioral changes are the earliest signs of a mental disorder, but arguably, the dynamics of brain function gets affected even earlier. Subsequently, spatio-temporal structure of disorder-specific dynamics is crucial for early diagnosis and understanding the disorder mechanism. A common way of learning discriminatory features relies on training a classifier and evaluating feature importance. Classical classifiers, based on handcrafted features are quite powerful, but suffer the curse of dimensionality when applied to large input dimensions of spatio-temporal data. Deep learning algorithms could handle the problem and a model introspection could highlight discriminatory spatio-temporal regions but need way more samples to train. In this paper we present a novel self supervised training schema which reinforces whole sequence mutual information local to context (whole MILC). We pre-train the whole MILC model on unlabeled and unrelated healthy control data. We test our model on three different disorders (i) Schizophrenia (ii) Autism and (iii) Alzheimers and four different studies. Our algorithm outperforms existing self-supervised pre-training methods and provides competitive classification results to classical machine learning algorithms. Importantly, whole MILC enables attribution of subject diagnosis to specific spatio-temporal regions in the fMRI signal.Comment: Accepted at MICCAI 2020. arXiv admin note: substantial text overlap with arXiv:1912.0313

Evaluating Acquisition Time of rfMRI in the Human Connectome Project for Early Psychosis. How Much Is Enough?

Resting-state functional MRI (rfMRI) correlates activity across brain regions to identify functional connectivity networks. The Human Connectome Project (HCP) for Early Psychosis has adopted the protocol of the HCP Lifespan Project, which collects 20 min of rfMRI data. However, because it is difficult for psychotic patients to remain in the scanner for long durations, we investigate here the reliability of collecting less than 20 min of rfMRI data. Varying durations of data were taken from the full datasets of 11 subjects. Correlation matrices derived from varying amounts of data were compared using the Bhattacharyya distance, and the reliability of functional network ranks was assessed using the Friedman test. We found that correlation matrix reliability improves steeply with longer windows of data up to 11–12 min, and ≥14 min of data produces correlation matrices within the variability of those produced by 18 min of data. The reliability of network connectivity rank increases with increasing durations of data, and qualitatively similar connectivity ranks for ≥10 min of data indicates that 10 min of data can still capture robust information about network connectivities

Retinotopic Maps, Spatial Tuning, and Locations of Human Visual Areas in Surface Coordinates Characterized with Multifocal and Blocked fMRI Designs

The localization of visual areas in the human cortex is typically based on mapping the retinotopic organization with functional magnetic resonance imaging (fMRI). The most common approach is to encode the response phase for a slowly moving visual stimulus and to present the result on an individual's reconstructed cortical surface. The main aims of this study were to develop complementary general linear model (GLM)-based retinotopic mapping methods and to characterize the inter-individual variability of the visual area positions on the cortical surface. We studied 15 subjects with two methods: a 24-region multifocal checkerboard stimulus and a blocked presentation of object stimuli at different visual field locations. The retinotopic maps were based on weighted averaging of the GLM parameter estimates for the stimulus regions. In addition to localizing visual areas, both methods could be used to localize multiple retinotopic regions-of-interest. The two methods yielded consistent retinotopic maps in the visual areas V1, V2, V3, hV4, and V3AB. In the higher-level areas IPS0, VO1, LO1, LO2, TO1, and TO2, retinotopy could only be mapped with the blocked stimulus presentation. The gradual widening of spatial tuning and an increase in the responses to stimuli in the ipsilateral visual field along the hierarchy of visual areas likely reflected the increase in the average receptive field size. Finally, after registration to Freesurfer's surface-based atlas of the human cerebral cortex, we calculated the mean and variability of the visual area positions in the spherical surface-based coordinate system and generated probability maps of the visual areas on the average cortical surface. The inter-individual variability in the area locations decreased when the midpoints were calculated along the spherical cortical surface compared with volumetric coordinates. These results can facilitate both analysis of individual functional anatomy and comparisons of visual cortex topology across studies