well, you could buy a faster machine :). The 6 days I don't think is normal. The subcortseg can take a long time, although on current opterons it's more like 15 hours I think. Check to make sure that you don't have a cerebellum attached in your filled volume (or ?h.orig surfaces), and that the skull isn't in these volumes either. The topology fixing scales as the square of the size of the largest defect, so it is fast for small defects and can be very slow if you have really big ones (which is what happens if you have cerebellum/skull attached).
cheers, Bruce
On Mon, 25 Sep 2006, Raksha Urs wrote:
Hello
We are running freesurfer on a Power Mac G4 with a 1.25 GHz processor and 1 GB Ram.
The subcortical segmentation procedure recon-all subcortseg -s <subjid> ran for 49 hours.
The rest of autorecon2 (recon-all -autorecon2-cp -s <subjid>) has been running for 6 days and is still working on the left hemisphere.
Is this normal?
Do you have any recommendations to speed up this process?
Thank you
Raksha Urs
Research Associate
Wien Center for Alzheimer's Disease and Memory Disorders
Mount Sinai Medical Center, Miami Beach FL