Michaël Sdika

Matthieu Martin, Bruno Sciolla, Michaël Sdika et al.

Preterm neonates are highly likely to suffer from ventriculomegaly, a dilation of the Cerebral Ventricular System (CVS). This condition can develop into life-threatening hydrocephalus and is correlated with future neuro-developmental impairments. Consequently, it must be detected and monitored by physicians. In clinical routing, manual 2D measurements are performed on 2D ultrasound (US) images to estimate the CVS volume but this practice is imprecise due to the unavailability of 3D information. A way to tackle this problem would be to develop automatic CVS segmentation algorithms for 3D US data. In this paper, we investigate the potential of 2D and 3D Convolutional Neural Networks (CNN) to solve this complex task and propose to use Compositional Pattern Producing Network (CPPN) to enable the CNNs to learn CVS location. Our database was composed of 25 3D US volumes collected on 21 preterm nenonates at the age of $35.8 \pm 1.6$ gestational weeks. We found that the CPPN enables to encode CVS location, which increases the accuracy of the CNNs when they have few layers. Accuracy of the 2D and 3D CNNs reached intraobserver variability (IOV) in the case of dilated ventricles with Dice of $0.893 \pm 0.008$ and $0.886 \pm 0.004$ respectively (IOV = $0.898 \pm 0.008$) and with volume errors of $0.45 \pm 0.42$ cm$^3$ and $0.36 \pm 0.24$ cm$^3$ respectively (IOV = $0.41 \pm 0.05$ cm$^3$). 3D CNNs were more accurate than 2D CNNs in the case of normal ventricles with Dice of $0.797 \pm 0.041$ against $0.776 \pm 0.038$ (IOV = $0.816 \pm 0.009$) and volume errors of $0.35 \pm 0.29$ cm$^3$ against $0.35 \pm 0.24$ cm$^3$ (IOV = $0.2 \pm 0.11$ cm$^3$). The best segmentation time of volumes of size $320 \times 320 \times 320$ was obtained by a 2D CNN in $3.5 \pm 0.2$ s.

Nima Hatami, Michaël Sdika, Hélène Ratiney

Magnetic resonance spectroscopy (MRS) is an important technique in biomedical research and it has the unique capability to give a non-invasive access to the biochemical content (metabolites) of scanned organs. In the literature, the quantification (the extraction of the potential biomarkers from the MRS signals) involves the resolution of an inverse problem based on a parametric model of the metabolite signal. However, poor signal-to-noise ratio (SNR), presence of the macromolecule signal or high correlation between metabolite spectral patterns can cause high uncertainties for most of the metabolites, which is one of the main reasons that prevents use of MRS in clinical routine. In this paper, quantification of metabolites in MR Spectroscopic imaging using deep learning is proposed. A regression framework based on the Convolutional Neural Networks (CNN) is introduced for an accurate estimation of spectral parameters. The proposed model learns the spectral features from a large-scale simulated data set with different variations of human brain spectra and SNRs. Experimental results demonstrate the accuracy of the proposed method, compared to state of the art standard quantification method (QUEST), on concentration of 20 metabolites and the macromolecule.

Pierre-Antoine Ganaye, Michaël Sdika, Hugues Benoit-Cattin

Semantic segmentation is an established while rapidly evolving field in medical imaging. In this paper we focus on the segmentation of brain Magnetic Resonance Images (MRI) into cerebral structures using convolutional neural networks (CNN). CNNs achieve good performance by finding effective high dimensional image features describing the patch content only. In this work, we propose different ways to introduce spatial constraints into the network to further reduce prediction inconsistencies. A patch based CNN architecture was trained, making use of multiple scales to gather contextual information. Spatial constraints were introduced within the CNN through a distance to landmarks feature or through the integration of a probability atlas. We demonstrate experimentally that using spatial information helps to reduce segmentation inconsistencies.