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
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 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:
- 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 ?
- 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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.
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):
- recon-all -s <subject> -autorecon1 -autorecon2
- 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):
- recon-all -s <subject> -autorecon1 -autorecon2
- 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.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 <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 > > > > > > > > > _______________________________________________ > 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.
Hi Nick I have a followup question about Scenario D:
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> -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 <subject> -autorecon1 -autorecon2 2. edit brainmask.mgz ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits) 3. recon-all -s <subject> *-autorecon3 (instead of -autorecon-pial)*
Thanks Mehul
On Wed, Mar 13, 2013 at 12:31 PM, Mehul Sampat mpsampat@gmail.com 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):
- recon-all -s <subject> -autorecon1 -autorecon2
- 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):
- recon-all -s <subject> -autorecon1 -autorecon2
- 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.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:
- 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
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@nmr.mgh.harvard.edu
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Mehul Sampat -
Nick Schmansky