FastSurfer 2.2.0

Merry X-mas Release! Happy to be able to give to you a new and shiny FastSurfer release.

We highly recommend users to upgrade to this release as it fixes the eTIV issue (see #378) which has been around since FastSurfer v1.1.0. In mainly 3T datasets we had quite different eTIV values compared to FreeSurfer and for some datasets these were far too small (e.g. HCP).

What are the Highlights of this Release

• Fixes the issue with eTIV #378
• Better bias field correction
• Similar to FreeSurfer it uses the 1.5 T default atlas for Talairach registration (for eTIV estimation)
• If you use 3T images, pass the -3T flat to run_fastsurfer.sh
• Improved way to build docker images with build script to reuse intermediate build steps
• Support for batch processing with new brun_fastsurfer.sh and SLURM integration with srun_fastsurfer.sh scripts
• Bump dependencies
• Lots of minor updates to code
• Improved documentation

What's Next

• Hypothalamus sub-segmentation module
• Olfactory bulb segmentation module
• Improved corpus callosum and fornix segmentation
• Further improvements and updates of the surface pipeline (reduced memory consumption)

As always, let us know via the issues if you find anything or have questions ...

What's Changed in Detail

• Consider local time formats when reading runtimes by @ClePol in #302
• Add and edit docstrings of recon_surf by @agirodi in #308
• fix intenstiy overflow in higher order interpolation in uchar by @m-reuter in #334
• Fix: imageio bug by @af-a in #338
• fix TypeError by @agirodi in #339
• Robustify mris_info string comparison to number of spaces (for FS741) by @af-a in #341
• Add version info for run_fastsurfer and into the docker image by @dkuegler in #327
• Add and edit Numpy docstrings by @agirodi in #332
• Upgrade: Ubuntu, Python, torch, Freesurfer, and other dependencies by @af-a in #348
• Update INSTALL.md by @dkuegler in #358
• Create a docker multistage build script by @dkuegler in #215
• Adding FreeSurfer commands (for validation tests) by @af-a in #362
• Fix: fspython environment variable by @af-a in #365
• Add fsaverage files for validation analyses by @af-a in #367
• added section contributing code by @m-reuter in #368
• fixing mid plane position by @m-reuter in #369
• fix align for highres by @m-reuter in #370
• fix the global normalization in bias field correction by @dkuegler in #387
• Fix the identification of the number of cpus by @dkuegler in #386
• add scripts for Fastsurfer orchestration on slurm clusters by @dkuegler in #388
• Bump versions of python packages by @dkuegler in #389
• Change a cpu_count instance that was left to get_num_threads by @dkuegler in #392
• Script to generate requirements files from docker image by @dkuegler in #400
• Add 3T atlas flag, remove mask from biasfield correction by @dkuegler in #406
• use nibabel read_geometry by @m-reuter in #411
• Fix memory limitation and subject/case globbing on slurm script by @dkuegler in #407
• Add support for expert options for singularity. by @dkuegler in #412
• "Small" changes to the CerebNet traning pipeline (missing apply_warp.py and shell errors in realistic_deformations) by @dkuegler in #415
• Update documentation for 2.2 Release by @dkuegler in #414
• PR for eTIV fix and new stable release by @m-reuter in #413

Full Changelog: v2.1.2...v.2.2.0