Hi Nick, Thank you very much. I have two followup questions. Since Scenario B is permissible, I believe the following two scenarios should also be allowed. (Just wanted to confirm this:)
Scenario C (for white matter edits):
1. recon-all -s <subject> -autorecon1 -autorecon2 2. edit wm.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits) 3. recon-all -s <subject> -autorecon2-wm -autorecon3
Scenario D (for pial edits): 1. recon-all -s <subject> -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s <subject> -autorecon2-pial
Basically, I am trying to see if I can avoid running -autorecon3 in the first run; make all the edits and then re-run recon-all with appropriate flags.
Thanks Mehul
On Wed, Mar 13, 2013 at 10:58 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
Mehul,
Scenerio B is permissible. And to address your question, the pial surface is created in the autorecon3 stage, making use of the parcellation data to refine it. I think a pial is generated during make_final_surfaces as its normal output, but its overwritten in autorecon3.
Nick
On Wed, 2013-03-13 at 10:52 -0700, Mehul Sampat wrote:
ps: just wanted to add a clarification to my question. The two scenarios are: Scenario A:
- recon-all -s <subject> -autorecon1 -autorecon2 -autorecon3
- add control points
- recon -all -s <subject> -autorecon2-cp -autorecon3
Scenario B:
- recon-all -s <subject> -autorecon1 -autorecon2
- add control points
- recon -all -s <subject> -autorecon2-cp -autorecon3
If Scenario B is permissible, the advantage is that, -autorecon3 is only run once thus saving a few hours of computation.
Thanks Mehul
On Wed, Mar 13, 2013 at 10:35 AM, Mehul Sampat mpsampat@gmail.com wrote: Hi Folks, Based on the tutorials, we normally run full recon-all pipeline; then add control points if required and then run -autorecon2-cp and -autorecon3 again.
Recently, I was looking at the process flow table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable and I have two questions: 1. From this table it seems like ?h.white is created in autorecon2 and ?h.pial is created in autorecon3. However, when i run recon-all -s subj -autorecon1 -autorecon2 i see that ?h.pial is also already created. Does this mean I am interpreting the process flow table incorrectly or is there an error in the table ? 2. Also if ?h.pial and ?h.white are already created at the end of autorecon2; then can we add control points at immediately after autorecon2 ? This way we would need to run autorecon3 only once and save resources. Or am I missing something and is it that one must run -autorecon2 and -autorecon3 and then add control points and then run -autorecon2-cp and -autorecon3 again. Thanks Mehul
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