FreeSurferSynthStripSkullStripScripted

FreeSurfer SynthStrip Skull Strip

Skull stripping using FreeSurfer's SynthStrip tool.

For a detailed description of SynthStrip please refer to its documentation here.

If you use SynthStrip in your analysis, please cite:

SynthStrip: Skull-Stripping for Any Brain Image Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl*, Malte Hoffmann* (*equal contribution) NeuroImage 260, 2022, 119474 https://doi.org/10.1016/j.neuroimage.2022.119474

Panels and their use

Input

• Input image: Image input volume to skull strip.

Output

• Stripped image: Stripped image output volume.

• Brain mask: Binary brain mask output volume.

Advanced

Advanced parameters are described in the SynthStrip documentation.

Tutorial

1. Download the "MRHead" sample data using the Sample Data module.

2. Switch to the FreeSurfer SynthStrip Skull Strip module.

3. Set the following parameters:

   • Input image: MRHead
   • Stripped image: Create new volume
   • Brain mask: Create new LabelMapVolume

4. Set advanced parameters as desired.

5. Click Apply.

The stripped image and brain mask will be saved in the new scalar volume and labelmap volume, respectively.