Hi Helen, That's a good question. You don't have to start at autorecon1, however. When you run -autorecon2-wm or -autorecon2-pial one of the first steps is: mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
which is changing the brain.finalsurfs.mgz to take into account the changes you made to the brainmask.mgz. Your edits are not lost. Allison -- On Thu, 11 Mar 2010, Helen Keefe wrote: > Hi, > > I have a similar questionto the one listed below. > After I edit brainmask.mgz and wm.mgz, my understanding was that I could > run > autorecon2-wm > > and would not have to run autorecon2-pial because -wm will run > everything else through the end of -autorecon2. > > However, if brainmask.mgz is run at the end of autorecon1, don't I need > to run autorecon1 again, since wm or contol point edits would alter the > brainmask?? > > Thanks for help, > Helen > > ____________________________________________________________ > > "Hi Dana, > > you can do autorecon2-cp and it will do both things (the wm comes after > it in the stream anyway) > > cheers > Bruce > On Tue, 9 Mar 2010, Dana W. Moore wrote: > >> Hello everyone, >> >> There is an image that needs white matter edits (editing voxels) as >> well as control points. I know the two commands I need to re-run are >> autorecon2-cp and autorecon2-wm. Can I do both kinds of edits and >> somehow combine the -cp and -wm commands, or do I need to do the >> control points first, re-run, and then do further white matter edits? >> >> Thanks, >> Dana >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
