neurotools-digest

FreeSurfer 8.1 (2025): Fast Setup & Your First recon-all on Mac and Ubuntu New to FreeSurfer or upgrading in 2025? In this guide I’ll show how to install FreeSurfer 8.x, set the license, run your first recon-all , and avoid common errors. The steps work on macOS (Intel/Apple Silicon), Ubuntu/WSL, and typical lab workstations. Covering the steps Download and install FreeSurfer 8.x (Mac: .pkg , Ubuntu: .deb ). Drop your license.txt in $HOME and set FS_LICENSE . Source SetUpFreeSurfer.sh and define SUBJECTS_DIR . Run recon-all -i T1.nii.gz -s Subj001 -all . QC in Freeview (white/pial surfaces, skull strip, segmentations). Download & Install (Mac / Ubuntu / WSL) Download FreeSurfer 8.1: Official FreeSurfer Download Page macOS (Intel or Apple Silicon) Download the latest FreeSurfer-8.x.x-macOS.pkg . Run the installer (default path is /Applications/freesurfer/8.x.x ). Open Terminal and source the setup script: export FREESURFER_HO...

Best AI Tools for Computational Neuroscience (Updated October 2025) Looking for the best AI tools and open‑source pipelines for EEG, MEG, fNIRS, and fMRI in 2025? This guide highlights the most reliable libraries and workflows researchers actually use—plus what changed after summer 2025. You’ll find practical picks, quickstart notes, and a simple decision path so you can build a robust analysis stack fast. Quick Picks by Use Case EEG/MEG preprocessing & visualization (Python): MNE‑Python EEG preprocessing & ICA (MATLAB): EEGLAB; MEG/EEG (MATLAB): FieldTrip Deep learning for EEG: Braindecode (PyTorch) fMRI preprocessing pipeline: fMRIPrep (with FreeSurfer) Statistical learning on neuroimaging: Nilearn (scikit‑learn compatible) Device‑agnostic acquisition / BCI prototyping: BrainFlow SDK + OpenBCI tools Benchmarking & open datasets: MOABB (EEG benchmarks) + OpenNeuro (BIDS datasets) Why these tools in 2025? Three things matter this y...