Re: [Freesurfer] Process flow: ReconAllDevTable
Hi Nick I have a followup question about Scenario D: Scenario D (for pial edits): 1. recon-all -s -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s -autorecon-pial I think -autorecon-pial is a subset of -autorecon3 ? Is so then could i still run -autorecon-pial without running -autorecon3? Or if i did this would i miss some of the outputs generated by -autorecon3. Also if -autorecon-pial is a subset of autorecon3, is the following scenario valid. Scenario E (for pial edits): 1. recon-all -s -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s *-autorecon3 (instead of -autorecon-pial)* Thanks Mehul On Wed, Mar 13, 2013 at 12:31 PM, Mehul Sampat wrote: > 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 -autorecon1 -autorecon2 > 2. edit wm.mgz ( > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits) > 3. recon-all -s -autorecon2-wm -autorecon3 > > Scenario D (for pial edits): > 1. recon-all -s -autorecon1 -autorecon2 > 2. edit brainmask.mgz ( > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) > 3. recon-all -s -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 -autorecon1 -autorecon2 -autorecon3 >> > 2. add control points >> > 3. recon -all -s -autorecon2-cp -autorecon3 >> > >> > >> > Scenario B: >> > 1. recon-all -s -autorecon1 -autorecon2 >> > 2. add control points >> > 3. recon -all -s -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 >> > 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. >> > > ___ 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 pe
Re: [Freesurfer] Process flow: ReconAllDevTable
Mehul, Correct, in both scenario C and D you do not need to include the -autorecon3 flag prior to making edits. For D, the kind of edits to brainmask necessary to fix the pial surface will be visible in the pial produced in -autorecon2 (which recall is not the final one, but will certainly expose brainmask-rooted pial problems). Nick On Wed, 2013-03-13 at 12:31 -0700, Mehul Sampat wrote: > 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 -autorecon1 -autorecon2 > 2. edit wm.mgz > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits) > 3. recon-all -s -autorecon2-wm -autorecon3 > > > Scenario D (for pial edits): > 1. recon-all -s -autorecon1 -autorecon2 > 2. edit brainmask.mgz > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) > 3. recon-all -s -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 > 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 -autorecon1 -autorecon2 > -autorecon3 > > 2. add control points > > 3. recon -all -s -autorecon2-cp -autorecon3 > > > > > > Scenario B: > > 1. recon-all -s -autorecon1 -autorecon2 > > 2. add control points > > 3. recon -all -s -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 > > > 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/co
Re: [Freesurfer] Process flow: ReconAllDevTable
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 -autorecon1 -autorecon2 2. edit wm.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits) 3. recon-all -s -autorecon2-wm -autorecon3 Scenario D (for pial edits): 1. recon-all -s -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s -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 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 -autorecon1 -autorecon2 -autorecon3 > > 2. add control points > > 3. recon -all -s -autorecon2-cp -autorecon3 > > > > > > Scenario B: > > 1. recon-all -s -autorecon1 -autorecon2 > > 2. add control points > > 3. recon -all -s -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 > > 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. > ___ 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.
Re: [Freesurfer] Process flow: ReconAllDevTable
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 -autorecon1 -autorecon2 -autorecon3 > 2. add control points > 3. recon -all -s -autorecon2-cp -autorecon3 > > > Scenario B: > 1. recon-all -s -autorecon1 -autorecon2 > 2. add control points > 3. recon -all -s -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 > 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 ___ 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.
Re: [Freesurfer] Process flow: ReconAllDevTable
ps: just wanted to add a clarification to my question. The two scenarios are: Scenario A: 1. recon-all -s -autorecon1 -autorecon2 -autorecon3 2. add control points 3. recon -all -s -autorecon2-cp -autorecon3 Scenario B: 1. recon-all -s -autorecon1 -autorecon2 2. add control points 3. recon -all -s -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 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.
[Freesurfer] Process flow: ReconAllDevTable
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.
