January 2006 FreeSurfer Release

Goals

• Post new 'stable' release, containing reliable auto-segmentation functionality, and bug fixes
• Make available open-source Freesurfer code (minus Numerical Recipes for C code)
• Basic automated testing of nightly-build 'dev' code base

Work Items

• aseg (xiao)

  • working to make aseg work for data originating from different pulse sequences or manufactuers than the training data used to build the atlas. currently, the subcortical atlas is built from Siemens scans, and the aseg results will be quite poor if the input data is from a GE scanner. we have sw that can improve this situation a lot, but it's not very stable, and this cross-sequence option will make the aseg on Siemens data worse. Estimated date of completion:

  • testing to optimize the default parameters for the subcortical segmentation. Estimated date of completion:

  • testing of a new subcortical atlas (asegs should be better than the current atlas). Estimated date of completion:

• recon-all improvements (doug)

  • linear pipeline: in recon-all, re-naming of stuff so that files don't get overwritten later in the stream. Estimated date of completion:

  • test accuracy of aseg and aparc w/ mri_pretess. Estimated date of completion:

• miscellaneous (doug)

  • total intercranial volume, using randy's method to align to talairach with skull. Estimated date of completion:

  • fixing tkmedit so that it implements -overlay-reg-identity properly. Estimated date of completion:

  • mri_surf2surf - mapping across hemispheres. Estimated date of completion:

  • mri_glmfit (new version of mris_glm) - mostly just need to document. Estimated date of completion:

  • mris_preproc - surface-based preprocessor script for mri_glmfit (does not exist but not hard). Estimated date of completion:

  • correction for multiple comparisons (mri_mcsim and mri_surfcluster). Estimated date of completion:

• talairach failure detection, incorporated into recon-all (nick, laurence, doug)

  • create Matlab-compiled binary and test in recon-all stream. Estimated date of completion:

  • code in C and test in recon-all stream. Estimated date of completion:

• automated testing of nightly build (kevin, nick)
• verifying talairach coordinates, when tal xform is known good, of: (nick, david)
  1. individual surfaces.
  2. individual volumes.
  3. average surfaces.
  4. average volumes.
• improve editing of wm with aseg (?)
• fix manual labelling (ev)