Wrapper scripts to perform brain extraction on BIDS datasets using fast deep learning tools like SynthStrip.
These scripts are designed to provide routine brain masking on a standing BIDS dataset.
Both SynthStrip and HD-BET are very easy to use. Run the containers directly to see usage for individual input images.
If using these masks in publications, please cite the appropriate papers:
Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl, Malte Hoffmann. SynthStrip: Skull-Stripping for Any Brain Image NeuroImage 2022, 260:119474
Isensee F, Schell M, Pflueger I, Brugnara G, Bonekamp D, Neuberger U, Wick A, Schlemmer HP, Heiland S, Wick W, Bendszus M, Maier-Hein KH, Kickingereder P. Automated brain extraction of multisequence MRI using artificial neural networks Hum Brain Mapping 2019, 40(17):4952-4964