Featured tool/resource
FreeSurfer
FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.
Featured tool/resource
BabelBrain: Planning software for Transcranial Ultrasound Stimulation
BabelBrain is an open-source standalone graphic-user-interface application designed for studies of neuromodulation using transcranial ultrasound stimulation (TUS). It calculates the transmitted acoustic field in the brain tissue, taking into account the distortion effects caused by the skull barrier. The simulation is prepared using scans from magnetic resonance imaging (MRI) and, if available, computed tomography (CT) and zero-echo time MRI scans. It also calculates the thermal effects based on a given ultrasound regime, such as the total duration of exposure, the duty cycle, and acoustic intensity. The tool is designed to work in tandem with neuronavigation and visualization software, such as 3DSlicer. BabelBrain supports multiple GPU backends, including Metal, OpenCL, and CUDA, and works on all major operating systems, including Linux, macOS, and Windows. This tool is particularly optimized for Apple ARM64 systems, which are common in brain imaging research.
Featured tool/resource
DeepISLES - Stroke Lesion Segmentation in MRI
DeepISLES is an advanced tool designed for the segmentation of ischemic stroke lesions in MRI. It accurately identifies and segments infarctions across various brain regions, encompassing a wide spectrum of sizes, ischemia counts, and patterns. Developed as part of the ISLES 2022 challenge, the algorithm operates on DWI, ADC, and optionally, FLAIR images.
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CONN : functional connectivity toolbox
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Seed-based d Mapping (SDM, formerly Signed Differential Mapping)
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