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Freesurfer

Overview

Freesurfer is a tool that algorithmically segments structural T1 images.

The Freesurfer user guide is extensive and includes installation instructions, command documentation, and tutortials.

Whole brain Freesurfer segmentation can be done with the following command:

Running Freesurfer 6.0 with Docker

For an automated script to run Freesurfer recon-all -all on your BIDS formatted data, see: https://github.com/muscbridge/freesurfer-6.0-docker

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