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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422