> For the complete documentation index, see [llms.txt](https://bridge-lab.gitbook.io/docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/segmentation/freesurfer.md).

# Freesurfer

## Overview

Freesurfer is a tool that algorithmically segments structural T1 images.

<figure><img src="/files/Sgy2Ek1RgIYv8N3fSjYr" alt="" width="375"><figcaption></figcaption></figure>

[The Freesurfer user guide](https://surfer.nmr.mgh.harvard.edu/fswiki) is extensive and includes installation instructions, command documentation, and tutortials.

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

```
recon-all -all -i [path]/T1.nii -s subj1
```

## 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>