Convolutional neural network MRI segmentation for fast and robust optimization of transcranial electrical current stimulation of the human brain

AbstractThe segmentation of structural MRI data is an essential step for deriving geometrical information about brain tissues. One important application is in transcranial electrical stimulation (e.g., tDCS), a non-invasive neuromodulatory technique where head modeling is required to determine the electric field (E-field) generated in the cortex to predict and optimize its effects. Here we propose a deep learning-based model (StarNEt) to automatize white matter (WM) and gray matter (GM) segmentation and compare its performance withFreeSurfer, an established tool. Since good definition of sulci and gyri in the cortical surface is an important requirement for E-field calculation,StarNEtis specifically designed to output masks at a higher resolution than that of the original input T1w-MRI.StarNEtuses a residual network as the encoder (ResNet) and a fully convolutional neural network with U-net skip connections as the decoder to segment an MRI slice by slice. Slice vertical location is provided as an extra input. The model was trained on scans from 425 patients in the open-access ADNI+IXI datasets, and usingFreeSurfersegmentation as ground truth. Model performance was evaluated using the Dice Coefficient (DC) in a separate subset (N=105) of ADNI+IXI and in two extra testing sets not involved in training. In addition,FreeSurferandStarNEtwere compared to manual segmentations of the MRBrainS18 dataset, also unseen by the model. To study performance in real use cases, first, we created electrical head models derived from theFreeSurferandStarNEtsegmentations and used them for montage optimization with a common target region using a standard algorithm (Stimweaver) and second, we usedStarNEtto successfully segment the brains of minimally conscious state (MCS) patients having suffered from brain trauma, a scenario whereFreeSurfertypically fails. Our results indicate thatStarNEtmatchesFreeSurferperformance on the trained tasks while reducing computation time from several hours to a few seconds, and with the potential to evolve into an effective technique even when patients present large brain abnormalities.