For those in the NMR center using the freesurfer dev environment, there will re a change in recon-all to use "new" atlaes by default. This change will be live on Monday.
The new cortical atlases are based on automatically filling ventricles and subcortical structures using the automatic subcortical segmentations (asegs). This is part of the "autorecon" stream accessed with the -autorecon flags (ie, -autorecon-all, -autorecon1, etc). The new subcortical atlas is based on 40 subjects.
To continue to use the old atlases, run recon-all with -old-atlas. If you use any of the "stage" flags (ie, -all, -stage1, -stage2, etc), recon-all will automatically use the old atlases to maintain consistency. Specifications of individual steps (eg, -surfreg) will use the new atlases.
To help keep track of which atlases were used, recon-all now stores he names of the atlases used for a subject in the following files located in the subject's scripts directory:
mri_em_register.atlas.dat - subcortical atlas (new=RB40_talairach_2005-07-20.gca, old=talairach_mixed.gca) mris_register.atlas.dat - cortical registration atlas (new=average.curvature.filled.buckner40.tif, old=average.tif) mris_ca_label.atlas.dat - cortical label atlas (new=curvature.buckner40.filled.desikan_killiany.gcs, old=atlas2002_simple.gcs)
If these files do not exist, then the old atlases are implied.
doug