FreeSurfer (2025): Install, License Setup & First Recon-All Guide
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...