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 <ni...@nmr.mgh.harvard.edu>wrote: > 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: > > 1. recon-all -s <subject> -autorecon1 -autorecon2 -autorecon3 > > 2. add control points > > 3. recon -all -s <subject> -autorecon2-cp -autorecon3 > > > > > > Scenario B: > > 1. recon-all -s <subject> -autorecon1 -autorecon2 > > 2. add control points > > 3. 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 <mpsam...@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 > > > > > > > > > > > > > > > > > > _______________________________________________ > > 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. >
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