it depends what you do. If you edit the wm.mgz to remove the connection you only need to run autorecon2-wm and autorecon3, which is a lot faster

cheers
Bruce

On Fri, 19 May 2017, miracle ozzoude wrote:

Hello Bruce, Thank you. Also, I don't need to run the entire pipeline again
just autorecon2 and autorecon3
Best, 
Paul

On Fri, May 19, 2017 at 11:41 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      it depends on how many connections there are
      On Fri, 19 May 2017, miracle ozzoude wrote:

            Hello Bruce, Is 2 or 3 slices ok? Also, after that I
            should run the rest of
            recon-all stage from autorecon2. 
            Best, 
            Paul

            On Fri, May 19, 2017 at 11:32 AM, Bruce Fischl
            <fischl@nmr.mgh.harvard.edu>
            wrote:
                  yes, or try rerunning watershed with different
            parameters. YOu
                  don't have to remove the entire skull that was
            left - just the
                  connection between it and wm
                  On Fri, 19 May 2017, miracle ozzoude wrote:

                        Hello Bruce, Yes, the skull is still
            attached.
                        Should I remove the skull for
                        all the slices and re-run it again?
                        Best, 
                        Paul

                        On Fri, May 19, 2017 at 10:28 AM, Bruce
            Fischl
                        <fischl@nmr.mgh.harvard.edu>
                        wrote:
                              Hi Paul

                              you need to look at the
            rh.orig.nofix and
                        rh.inflated.nofix.
                              Typically something big is wrong
            like skull
                        attached to brain or
                              something

                              cheers
                              Bruce


                              On Fri, 19 May 2017, miracle
            ozzoude wrote:

                                    Hello Freesurfer
            expert, While running
                        recon-all on
                                    one of my subjects, the
                                    pipeline got stuck during
            the "fix
                        topology rh"
                                    stage for almost 12hrs. How
                                    do I diagnosis the problem
            and fix it? I
                        have
                                    attached the recon-all.log
                                    file. Thank you
                                    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.