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

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.Comment: This work has been submitted to ISBI 201

PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI

In this paper we present a novel method for the correction of motion artifacts that are present in fetal Magnetic Resonance Imaging (MRI) scans of the whole uterus. Contrary to current slice-to-volume registration (SVR) methods, requiring an inflexible anatomical enclosure of a single investigated organ, the proposed patch-to-volume reconstruction (PVR) approach is able to reconstruct a large field of view of non-rigidly deforming structures. It relaxes rigid motion assumptions by introducing a specific amount of redundant information that is exploited with parallelized patch-wise optimization, super-resolution, and automatic outlier rejection. We further describe and provide an efficient parallel implementation of PVR allowing its execution within reasonable time on commercially available graphics processing units (GPU), enabling its use in the clinical practice. We evaluate PVR's computational overhead compared to standard methods and observe improved reconstruction accuracy in presence of affine motion artifacts of approximately 30% compared to conventional SVR in synthetic experiments. Furthermore, we have evaluated our method qualitatively and quantitatively on real fetal MRI data subject to maternal breathing and sudden fetal movements. We evaluate peak-signal-to-noise ratio (PSNR), structural similarity index (SSIM), and cross correlation (CC) with respect to the originally acquired data and provide a method for visual inspection of reconstruction uncertainty. With these experiments we demonstrate successful application of PVR motion compensation to the whole uterus, the human fetus, and the human placenta.Comment: 10 pages, 13 figures, submitted to IEEE Transactions on Medical Imaging. v2: wadded funders acknowledgements to preprin

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Deep grey matter volumetry as a function of age using a semi-automatic qMRI algorithm

Quantitative Magnetic Resonance has become more and more accepted for clinical trial in many fields. This technique not only can generate qMRI maps (such as T1/T2/PD) but also can be used for further postprocessing including segmentation of brain and characterization of different brain tissue. Another main application of qMRI is to measure the volume of the brain tissue such as the deep Grey Matter (dGM). The deep grey matter serves as the brain's "relay station" which receives and sends inputs between the cortical brain regions. An abnormal volume of the dGM is associated with certain diseases such as Fetal Alcohol Spectrum Disorders (FASD). The goal of this study is to investigate the effect of age on the volume change of the dGM using qMRI. Thirteen patients (mean age= 26.7 years old and age range from 0.5 to 72.5 years old) underwent imaging at a 1.5T MR scanner. Axial images of the entire brain were acquired with the mixed Turbo Spin-echo (mixed -TSE) pulse sequence. The acquired mixed-TSE images were transferred in DICOM format image for further analysis using the MathCAD 2001i software (Mathsoft, Cambridge, MA). Quantitative T1 and T2-weighted MR images were generated. The image data sets were further segmented using the dual-space clustering segmentation. Then volume of the dGM matter was calculated using a pixel counting algorithm and the spectrum of the T1/T2/PD distribution were also generated. Afterwards, the dGM volume of each patient was calculated and plotted on scatter plot. The mean volume of the dGM, standard deviation, and range were also calculated. The result shows that volume of the dGM is 47.5 ±5.3ml (N=13) which is consistent with former studies. The polynomial tendency line generated based on scatter plot shows that the volume of the dGM gradually increases with age at early age and reaches the maximum volume around the age of 20, and then it starts to decrease gradually in adulthood and drops much faster in elderly age. This result may help scientists to understand more about the aging of the brain and it can also be used to compare with the results from former studies using different techniques

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Registration of 3D fetal neurosonography and MRI.

We propose a method for registration of 3D fetal brain ultrasound with a reconstructed magnetic resonance fetal brain volume. This method, for the first time, allows the alignment of models of the fetal brain built from magnetic resonance images with 3D fetal brain ultrasound, opening possibilities to develop new, prior information based image analysis methods for 3D fetal neurosonography. The reconstructed magnetic resonance volume is first segmented using a probabilistic atlas and a pseudo ultrasound image volume is simulated from the segmentation. This pseudo ultrasound image is then affinely aligned with clinical ultrasound fetal brain volumes using a robust block-matching approach that can deal with intensity artefacts and missing features in the ultrasound images. A qualitative and quantitative evaluation demonstrates good performance of the method for our application, in comparison with other tested approaches. The intensity average of 27 ultrasound images co-aligned with the pseudo ultrasound template shows good correlation with anatomy of the fetal brain as seen in the reconstructed magnetic resonance image