freesurfer/synthstrip repository overview

⁠SynthStrip

SynthStrip is a skull-stripping tool designed to extract the brain from various medical imaging modalities, spanning contrasts, resolutions, and diverse subject populations. It leverages a deep-learning strategy that synthesizes extremely variable training images from segmentation maps, enabling the model to generalize across acquisition protocols.

For details on SynthStrip and how to use the Docker image, visit synthstrip.io⁠.

⁠Changes

• synthstrip:1.8, latest⁠
  synthstrip:1.8-gpu⁠
  - add procps⁠ to the Docker images
  - revert normalization to avoid torch.quantile error⁠
  - control and report background-fill value

• synthstrip:1.7, latest⁠
  synthstrip:1.7-gpu⁠
  - introduce separate CPU-only and GPU images⁠
  - switch from Ubuntu to minimal Python base image⁠
  - add option to control the number of CPU threads
  - set up automated tests

• synthstrip:1.6⁠
  - add support for large borders
  - resolve NumPy deprecation warning
  - add option to save the distance transform

• synthstrip:1.5⁠
  - support multi-frame images
  - save output files as regular user with Docker
  - avoid waiting for PyTorch only to show help text

• synthstrip:1.4⁠
  - fix floating-point error in output voxel size⁠
  - switch from CentOS to Ubuntu base image

• synthstrip:1.3⁠
  - fix output images appearing shifted in ITK-SNAP⁠

• synthstrip:1.2⁠
  - fix qform/sform handling in surfa⁠
  - add model for predicting brain masks without CSF

• synthstrip:1.1⁠
  - resolve SciPy deprecation warning
  - switch from freesurfer to surfa package
  - print help text when no arguments provided

• synthstrip:1.0⁠
  - release initial image

⁠Contact

Reach out to the FreeSurfer mailing list⁠ or open an issue on GitHub⁠.