Jordan, The -subcortseg step is going to be looking for inputs that were created before it, so you can't really skip the steps before it. I suppose you can skip the surface steps afterwards as long as you understand that the aseg.mgz will not give you accurate wm and gm volumes.
In order to get the volume stats, you need to run the -segstats step in -autorecon3. I'm not sure if you will get any complaints for missing files from not running the surfaces. I'm also not sure if there is anything in the longitudinal processing stream that would complain about this method - but hopefully Martin or Nick will chime in about that. Allison -- On Thu, 15 Apr 2010, Jordan Poppenk wrote: > Dear list, > > I am about to start processing a largish longitudinal dataset and wondered > whether I could save some processing time in the following ways: > > 1) I have seen written in a few places that only norm.mgz is used from the > cross-sectional stream during base template creation at the next stage. Does > that mean I can run "-autorecon1" only on each of the timepoints during the > cross-sectional processing stage rather than "-all"? > 2) As I am only interested in the subcortical output of the longitudinal > processing, can I include the flags "-autorecon1 -subcortseg" in all > remaining steps in the longitudinal stream to skip cortical processing, or > will that cause problems? > > Thanks for your help, > Jordan > _______________________________________________ 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.
