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| Robust, universal skull-stripping for brain images of any type. <<BR>> {{attachment:skullstrips.png||height="250"}} <<BR>> 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 [[FreeSurferSupport|mailing list]]. == 1. Overview == This wiki page still a work-in-progress. == 2. Installation == We offer two ways of run !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 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 == 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. |
'''''Robust, universal brain-extraction for images of any type. SynthStrip documentation has been moved to [[https://surfer.nmr.mgh.harvard.edu/docs/synthstrip]].''''' |
SynthStrip
Robust, universal brain-extraction for images of any type. SynthStrip documentation has been moved to https://surfer.nmr.mgh.harvard.edu/docs/synthstrip.