We have worked hard to bring you this new and awesome release v1.1 !!
After weeks of thorough testing we are finally happy with this version of FastSurfer, which is based on FreeSurfer 7.2 now. Over-and-over we repeated a battery of tests (including accuracy to a ground truth set, test-retest reliability, group separability, and run-time performance). Not only are we seeing the same high-quality of results as our 1.0 release, we can bring that to you at a faster speed.
What has changed in v1.1
- We upgraded our dependencies, most notably we use:
- FreeSurfer 7.2
- Ubuntu 20.4 (in Docker)
- Upgrades of other dependencies (Python packages, NVIDIA)
- We reduced our Docker image sizes significantly (via a 2-stage build and striping unnecessary files)
- We now have pre-built images on Docker Hub and documentation on how to run Singularity
- Faster N4 bias field correction using simpleITK
- Improved search for CorpusCallosum (mid plane finding)
- Replace and speed-up global spherical registration (rotation) in FS7.2 mris_register
Detailed commits: https://github.com/Deep-MI/FastSurfer/commits/v1.1.0
We thank all the contributors for their help!!
Roadmap
- Include FastSurferVINN for high-res segmentation (for v2.0, ongoing)
- Update recon-surf pipeline to high-res (for v2.0, done)
- Further speed-up, e.g. by a more efficient mapping of BA-labels etc (for v2.1 or earlier, done)
- CC/Fornix segmentation CNN (and mid plane finding) (for v2.* or 3.0)
- Integration of other segmentation modules (for v2.* or v3.0)
- CerebNet for cerebellum sub-segmentation
- Olfactory bulb segmentation
- Hypothalamus sub-segmentation
- Unify interface and merge segmentations if possible (v3.0)
- Improved surface processing (construction, registration with DL) (for v4.0)
- Restructuring of recon-surf as modern pipeline (e.g. Nextflow or Snakemake) (anytime)
- Automatisation of releasing Docker images on Dockerhub (CI, e.g. via Travis or Github Actions) (anytime)