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LeHenschel authored and m-reuter committed Jun 24, 2020
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Expand Up @@ -14,7 +14,7 @@ The *FastSurferCNN* and *recon_surf* directories contain all the source code and

There are two ways to run FastSurfer - (a) locally or (b) using Docker.

(a) For a local version, download this github repository (use git clone or download as zip and unpack) for the necessary source code and python scripts. If you also have the necessary python libraries installed (see above), this is already enough to generate the whole-brain segmentation using FastSurferCNN (see the README.md in the FastSurferCNN directory for the exact commands). In order to run the whole FastSurfer pipeline locally on your machine, a working version of __FreeSurfer__ (v6.0) is needed (specifically to run recon-surf). See [Example 1](#example-1:-fastSurfer-on-subject1) and [Example 2](#example-2:-fastSurfer-on-multiple-subjects-(parallel-processing)) for an illustration of the commands to run the entire FastSurfer pipeline (FastSurferCNN + recon-surf) locally.
(a) For a local version, download this github repository (use git clone or download as zip and unpack) for the necessary source code and python scripts. If you also have the necessary python libraries installed (see above), this is already enough to generate the whole-brain segmentation using FastSurferCNN (see the README.md in the FastSurferCNN directory for the exact commands). In order to run the whole FastSurfer pipeline locally on your machine, a working version of __FreeSurfer__ (v6.0, https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads) is needed (specifically to run recon-surf). See [Example 1](#example-1:-fastSurfer-on-subject1) and [Example 2](#example-2:-fastSurfer-on-multiple-subjects-(parallel-processing)) for an illustration of the commands to run the entire FastSurfer pipeline (FastSurferCNN + recon-surf) locally.

(b) For a dockerized version, simply use the provided Dockerfiles in our Docker directory to build your image (see the README.md in the Docker directory). No other local installations are needed (FreeSurfer and everything else is already included). See [Example 3](#example-3:-fastSurfer-inside-docker) for a working example.

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