Hi Allison,

But when I run -autorecon-cp it complains that the option does not exist. I'm using FS5.1..

msteenwj@lnx-rad-03 freesurfer51 % recon-all -subjid P102_corr -autorecon-cp ERROR: Flag -autorecon-cp unrecognized. -subjid P102_corr -autorecon-cp Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s P102_corr exited with ERRORS at Fri Mar 2 14:23:15 CET 2012

For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Best, Martijn

On Fri, Mar 2, 2012 at 2:15 PM, Allison Stevens Player < astevens@nmr.mgh.harvard.edu> wrote:

Hi Martijn, autorecon-cp is correct, we start the process a bit earlier now. But even better, regardless of what edits you make, you can rerun with "recon-all -make all" and it will start at the earliest needed step. (Although running from autorecon2 after the skullstrip fix is correct as well). Allison

On Mar 2, 2012, at 6:11 AM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:

Dear all,

On http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is indicated that -autorecon-cp should be added if control points are added. Shouldn't this be -autorecon2-cp?

Furthermore, suppose control points are added and -autorecon2-cp has been runned. If I then correct the skull strip (as indicated in the wiki) and want to rerun, do I have to call -autorecon2-cp then, or can I just run -autorecon2 -autorecon3?

Best, Martijn

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I tried that, but then it also runs steps from autorecon1 (tailararch check, nu, etc)

On Fri, Mar 2, 2012 at 2:40 PM, Allison Stevens Player < astevens@nmr.mgh.harvard.edu> wrote:

Okay, I'll look into it and fix the wiki page if needed. However, -make all should do the same for you. Allison

On Mar 2, 2012, at 8:23 AM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:

Hi Allison,

But when I run -autorecon-cp it complains that the option does not exist. I'm using FS5.1..

msteenwj@lnx-rad-03 freesurfer51 % recon-all -subjid P102_corr -autorecon-cp ERROR: Flag -autorecon-cp unrecognized. -subjid P102_corr -autorecon-cp Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s P102_corr exited with ERRORS at Fri Mar 2 14:23:15 CET 2012

For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Best, Martijn

On Fri, Mar 2, 2012 at 2:15 PM, Allison Stevens Player < astevens@nmr.mgh.harvard.edu> wrote:

...

Hi Martijn, autorecon-cp is correct, we start the process a bit earlier now. But even better, regardless of what edits you make, you can rerun with "recon-all -make all" and it will start at the earliest needed step. (Although running from autorecon2 after the skullstrip fix is correct as well). Allison

On Mar 2, 2012, at 6:11 AM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:

Dear all,

On http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is indicated that -autorecon-cp should be added if control points are added. Shouldn't this be -autorecon2-cp?

Furthermore, suppose control points are added and -autorecon2-cp has been runned. If I then correct the skull strip (as indicated in the wiki) and want to rerun, do I have to call -autorecon2-cp then, or can I just run -autorecon2 -autorecon3?

Best, Martijn

---

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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.

Okay :-). Last question then, how about skull strip correction.

If I understood well, it is advisable to first add control points and then correct the skull strip. Will the option set -autorecon2 -autorecon3 (as indicated in the wiki to be runned after manual skull strip correction) also recognize the existence of the control points, or is it then needed to run -autorecon2-cp again?

Best, Martijn

On Fri, Mar 2, 2012 at 2:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Martin

yes, you are right, that is a typo. And rerunning autorecon2 is sufficient since it is a superset of autorecon2-cp (and will detect the existence of control points, and use them)

cheers Bruce

On Fri, 2 Mar 2012, Martijn Steenwijk wrote:

Dear all,

...

On http://surfer.nmr.mgh.**harvard.edu/fswiki/**RecommendedReconstructionhttp://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is indicated that -autorecon-cp should be added if control points are added. Shouldn't this be -autorecon2-cp?

Furthermore, suppose control points are added and -autorecon2-cp has been runned. If I then correct the skull strip (as indicated in the wiki) and want to rerun, do I have to call -autorecon2-cp then, or can I just run -autorecon2 -autorecon3?

Best, Martijn

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/**compliancelinehttp://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.

Ok, thanks!

On Fri, Mar 2, 2012 at 2:37 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

yes, it will recognize and use the control points. autorecon2-cp is a subset of autorecon2 so no need to rerun it.

cheers Bruce

On Fri, 2 Mar 2012, Martijn Steenwijk wrote:

Okay :-). Last question then, how about skull strip correction.

...

If I understood well, it is advisable to first add control points and then correct the skull strip. Will the option set -autorecon2 -autorecon3 (as indicated in the wiki to be runned after manual skull strip correction) also recognize the existence of the control points, or is it then needed to run -autorecon2-cp again?

Best, Martijn

On Fri, Mar 2, 2012 at 2:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Martin

 yes, you are right, that is a typo. And rerunning autorecon2 is

sufficient since it is a superset of autorecon2-cp (and will detect the existence of control points, and use them)

 cheers
 Bruce

On Fri, 2 Mar 2012, Martijn Steenwijk wrote:

 Dear all,
 On http://surfer.nmr.mgh.**harvard.edu/fswiki/**

RecommendedReconstructionhttp://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is indicated that -autorecon-cp should be added if control points are added. Shouldn't this be -autorecon2-cp?

 Furthermore, suppose control points are added and -autorecon2-cp has

been runned. If I then correct the skull strip (as indicated in the wiki) and want to rerun, do I have to call -autorecon2-cp then, or can I just run -autorecon2 -autorecon3?

 Best,
 Martijn

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/**compliancelinehttp://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.