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We offer two ways of run !SynthStrip: within !FreeSurfer or as a standalone command-line tool.

'''''Within !FreeSurfer:''''' As of March 1 2022, SynthStrip is available in the dev (nightly) !FreeSurfer distributions and will be included in the upcoming !FreeSurfer v7.3 release.

'''''Standalone Utility:''''' If you do not want to install an entire !FreeSurfer distribution to run !SynthStrip, you can install a singular, pre-built macOS or linux !SynthStrip executable. To do this, download the maxOS or linux file from this source.

SynthStrip

This functionality is only available in the development version of FreeSurfer. Rather than directly contacting the author, please post your questions on this module to the FreeSurfer mailing list.


skullstrips.png

1. Overview

2. Installation

We offer two ways of run SynthStrip: within FreeSurfer or as a standalone command-line tool.

Within FreeSurfer: As of March 1 2022, SynthStrip is available in the dev (nightly) FreeSurfer distributions and will be included in the upcoming FreeSurfer v7.3 release.

Standalone Utility: If you do not want to install an entire FreeSurfer distribution to run SynthStrip, you can install a singular, pre-built macOS or linux SynthStrip executable. To do this, download the maxOS or linux file from this source.

3. Usage

Once installed, you can run SynthStrip with the following:

synthstrip -i <input> -o <stripped>

In this command, <input> represents the path to the input image and <stripped> is the skull-stripped output. To also save the corresponding brain mask, the -m command line flag can be used to specify the mask output path. For additional options and command description, please use the --help flag. For the large majority of images with voxel sizes near 1 mm^3, SynthStrip should run in less than 1 minute on the CPU. As image size (or resolution) increases, this runtime might increase as well.

4. Evaluation Dataset

SynthStrip (last edited 2022-05-02 08:57:53 by AndrewHoopes)