I mean there will be no subsequent command that turn of the use of control points in the aseg

cheers
Bruce


On Thu, 14 Sep 2017, miracle ozzoude wrote:

Thanks Bruce. resetting means, all my changes will be incorporated into the final output files? 
Best, 
Paul

On Thu, Sep 14, 2017 at 3:52 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      I'm not sure it matters, but if you put it at the end nothing will reset it
      On Thu, 14 Sep 2017, miracle ozzoude wrote:

            Hello Bruce,
            Yes, that is my end goal. I have a patient i edited the aseg to include
            left-cerebral white matter
            and also, want to normalize the intensity using expert option. Where should
            I place the
            "-canorm-usecps" flag ? After the command like " recon-all -autorecon2
            -autorecon3 -expert -parallel
            -openmp 8 -bigventricles -3T time -canorm-usecps" or before autorecon2 like
            "recon-all -autorecon2
            -canorm-usecps -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T
            time. Thank you.

            Best, 
            Paul 

            On Thu, Sep 14, 2017 at 3:17 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
            wrote:
                  do you want the control points to be applied to the aseg? If so, you
            need to also
                  specify -canorm-usecps

                  cheers
                  Bruce
                  On Thu, 14 Sep 2017, miracle ozzoude wrote:

                        Thanks Bruce. Yes, I want to regenerate the aseg and also use
            the expert
                        option for control point.
                        That's recon-all -autorecon2 -autorecon3 -expert -parallel
            -openmp 8
                        -bigventricles -3T time. 
                        Best, 
                        Paul

                        On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl
            <fischl@nmr.mgh.harvard.edu>
                        wrote:
                              do you want it to regenerate the aseg? If not, then a). If
            so, then
                        you would just run
                              autorecon2 (instead of autorecon2-cp)

                              cheers
                              Bruce
                              On Thu, 14 Sep 2017, miracle ozzoude wrote:

                                    I used the expert option for control points and
            manually edited
                        the
                                    aseg.presurf.mgz. Which is the
                                    proper flag to use in other to incorporate the
            respective
                        changes? 
                                    a) recon-all -autorecon2-cp -autorecon2-noaseg
            -autorecon3
                        -expert -parallel
                                    -openmp 8
                                    -bigventricles -3T -time

                                    or 

                                    b) recon-all -autorecon2-cp -autorecon3 -expert
            -parallel
                        -openmp 8
                                    -bigventricles -3T -time

                                    Thanks. 

                                    Best, 
                                    Paul



                        _______________________________________________
                        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.




_______________________________________________
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.