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.
1. Overview
2. Installation
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.