Olli Gröhn

Julian Rasch, Ville Kolehmainen, Riikka Nivajärvi et al.

The goal of dynamic magnetic resonance imaging (dynamic MRI) is to visualize tissue properties and their local changes over time that are traceable in the MR signal. We propose a new variational approach for the reconstruction of subsampled dynamic MR data, which combines smooth, temporal regularization with spatial total variation regularization. In particular, it furthermore uses the infimal convolution of two total variation Bregman distances to incorporate structural a-priori information from an anatomical MRI prescan into the reconstruction of the dynamic image sequence. The method promotes the reconstructed image sequence to have a high structural similarity to the anatomical prior, while still allowing for local intensity changes which are smooth in time. The approach is evaluated using artificial data simulating functional magnetic resonance imaging (fMRI), and experimental dynamic contrast-enhanced magnetic resonance data from small animal imaging using radial golden angle sampling of the k-space.

Juan Miguel Valverde, Artem Shatillo, Riccardo de Feo et al.

We present a fully convolutional neural network (ConvNet), named RatLesNetv2, for segmenting lesions in rodent magnetic resonance (MR) brain images. RatLesNetv2 architecture resembles an autoencoder and it incorporates residual blocks that facilitate its optimization. RatLesNetv2 is trained end to end on three-dimensional images and it requires no preprocessing. We evaluated RatLesNetv2 on an exceptionally large dataset composed of 916 T2-weighted rat brain MRI scans of 671 rats at nine different lesion stages that were used to study focal cerebral ischemia for drug development. In addition, we compared its performance with three other ConvNets specifically designed for medical image segmentation. RatLesNetv2 obtained similar to higher Dice coefficient values than the other ConvNets and it produced much more realistic and compact segmentations with notably fewer holes and lower Hausdorff distance. The Dice scores of RatLesNetv2 segmentations also exceeded inter-rater agreement of manual segmentations. In conclusion, RatLesNetv2 could be used for automated lesion segmentation, reducing human workload and improving reproducibility. RatLesNetv2 is publicly available at https://github.com/jmlipman/RatLesNetv2.

Juan Miguel Valverde, Artem Shatillo, Riccardo de Feo et al.

Manual segmentation of rodent brain lesions from magnetic resonance images (MRIs) is an arduous, time-consuming and subjective task that is highly important in pre-clinical research. Several automatic methods have been developed for different human brain MRI segmentation, but little research has targeted automatic rodent lesion segmentation. The existing tools for performing automatic lesion segmentation in rodents are constrained by strict assumptions about the data. Deep learning has been successfully used for medical image segmentation. However, there has not been any deep learning approach specifically designed for tackling rodent brain lesion segmentation. In this work, we propose a novel Fully Convolutional Network (FCN), RatLesNet, for the aforementioned task. Our dataset consists of 131 T2-weighted rat brain scans from 4 different studies in which ischemic stroke was induced by transient middle cerebral artery occlusion. We compare our method with two other 3D FCNs originally developed for anatomical segmentation (VoxResNet and 3D-U-Net) with 5-fold cross-validation on a single study and a generalization test, where the training was done on a single study and testing on three remaining studies. The labels generated by our method were quantitatively and qualitatively better than the predictions of the compared methods. The average Dice coefficient achieved in the 5-fold cross-validation experiment with the proposed approach was 0.88, between 3.7% and 38% higher than the compared architectures. The presented architecture also outperformed the other FCNs at generalizing on different studies, achieving the average Dice coefficient of 0.79.