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
- Input image: Image input volume to skull strip.
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Stripped image: Stripped image output volume.
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Brain mask: Binary brain mask output volume.
Advanced parameters are described in the SynthStrip documentation.
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Download the "MRHead" sample data using the Sample Data module.
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Switch to the FreeSurfer SynthStrip Skull Strip module.
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Set the following parameters:
- Input image: MRHead
- Stripped image: Create new volume
- Brain mask: Create new LabelMapVolume
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Set advanced parameters as desired.
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Click Apply.
The stripped image and brain mask will be saved in the new scalar volume and labelmap volume, respectively.