Hi,
I have a few questions about the process flow for the last stable build (5.0.0). After looking over http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all , https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable , and http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags , it looks like there's some inconsistency in the info on these pages that's left me a bit confused about what processing steps are and aren't invoked by autorecon2-wm, and autorecon-pial.
On the 'Other Useful Flags' page, it looks as though autorecon2-wm doesn't invoke maskbfs / mri_mask, but on the recon-all page as well as in the mailing list archives it's said that autorecon2-wm runs processes both prior to autorecon2-pial and including the processes called on by autorecon2-pial. (By the way, is autorecon-pial a separate command from autorecon2-pial? Is the only difference that the former runs all the autorecon3 steps whereas the latter ends at the last step of autorecon2?) If autorecon2-wm doesn't run maskbfs / mri_mask, then wouldn't a subject who has both had pial edits done to their brainmask.mgz and wm edits done to their wm.mgz end up generating parcellation stats that don't reflect the pial edits? If that's the case, then would adding a -maskbfs flag before autorecon2-wm and -autorecon3 solve the problem?
And autorecon2-cp starts with -normalization2, right? On the http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction page it says that it starts running at -normalization, which would be far earlier in the pipeline.
Finally, should one always wait to make pial edits or WM edits after adding control points and reprocessing from autorecon2-cp? It looks to me as though throwing control points and WM edits and/or pial edits simultaneously at a reprocessing stream wouldn't pose any problems for the file dependencies, but that you might be able to do better pial and/or WM edits after seeing the newly generated surfaces and the newly segmented wm.mgz after recon-all has incorporated the control points.
Thanks so much for your help!
Warren
-- Warren Winter Research Coordinator Children's Hospital Boston Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224