is there a minimum number of flags to specify in recon if all you want to do is surface analysis on some structural images?
doing this locally, we've got space issues on the cluster. takes about 20hrs. want to cut down on that. how long does a full recon-all take on the cluster?
I did a full freesurfer recon on the cluster last week and it took 18 hours to get to the finished pial surfaces, and 4 hours more to finish the spherical surfaces. You can cut that down if you know you don't want the spheres. Even more if you want to skip some of the refinement steps that clean up the surfaces. But I don't recommend that. The autorecon-all script was a big step forward because messing with separate options is a headache. Unless you are in a hurry I would just let it run overnight. If you really don't want to have freesurfer do its normal full recon you will need to know which parts you do want and which you don't. When you say "all you want to do is surface analysis on structural images" that sounds like what freesurfer is for, so it's not clear what you could leave out.
if you look at the recon-all help, you can see the full list/order of processes:
Autorecon Processing Stages (see -autorecon# flags above): 1. Motion Correction and Conform 2. NU (Non-Uniform intensity normalization) 3. Talairach transform computation 4. Intensity Normalization 1 5. Skull Strip
6. EM Register (linear volumetric registration) 7. CA Intensity Normalization 8. CA Non-linear Volumetric Registration 9. Remove neck 10. EM Register, with skull 11. CA Label (Aseg: Volumetric Labeling) and Statistics
12. Intensity Normalization 2 (start here for control points) 13. White matter segmentation 14. Edit WM With ASeg 15. Fill (start here for wm edits) 16. Tessellation (begins per-hemisphere operations) 17. Smooth1 18. Inflate1 19. QSphere 20. Automatic Topology Fixer 21. Final Surfs (start here for brain edits for pial surf) 22. Smooth2 23. Inflate2
freesurfer questions
Posted - Feb 04 2011 : 2:49:30 PM
