• SynthStrip

SynthStrip

Robust, universal skull-stripping for brain images of any type.

Note: this functionality is currently 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.

1. Overview

This wiki page is still a work-in-progress.

2. Installation

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

Within FreeSurfer: As of March 14 2022, SynthStrip is available in the dev (nightly) FreeSurfer distributions and will be included in the upcoming FreeSurfer v7.3 release.

Standalone Utility: Coming soon! 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 mm³, 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

In the SynthStrip publication, we gather a large test set, from a collection of public datasets, that spans across acquisition type, age, and health. We plan to make this subset of images, along with ground-truth brain mask labels, available for download in the near future.