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
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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:
- 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