Re: [Freesurfer] Optic chiasm resisting edits

make sure it creates the filled without error, and if so, check the filled to make sure that the edits to the wm are present in it (I don't know why they wouldn't be though....) On Tue, 31 Jul 2012, Peter McNally wrote:

Whoops forgot to select reply all... Yes I am erasing the chiasm using tkmedit--I'll rerun autorecon-wm now and send the recon-all.log results when they finish (probably) tomorrow.

Thank you, Peter

On Tue, Jul 31, 2012 at 2:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you cc the list on these emails? And try rerunning autorecon2-wm and send us the recon-all.log results? You are erasing the chiasm using tkmedit, aren't you?

  On Tue, 31 Jul 2012, Peter McNally wrote:

        The edits do not appear to be reflected in the
        filled.mgz (the chiasm is
        still present on the filled.mgz volume). The same is
        true for ?h.orig, and
        they are even worse than normal on ?h.orig.nofix.

        On Tue, Jul 31, 2012 at 2:14 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              hmmm. And are the edits reflected in the
        filled.mgz? Is the
              chiasm gone? How about in the ?h.orig and
        ?h.orig.nofix?
              On Tue, 31 Jul 2012, Peter McNally wrote:

                    Hi Bruce,

                    Thank you for your speedy response. Yes,
        I ran
                    -autorecon2-wm -autorecon3.

                    Best,
                    Peter

                    On Tue, Jul 31, 2012 at 2:03 PM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          Hi Peter
                          what did you run after editing it
        out of the
                    wm.mgz? You should
                          be running -autorecon2-wm
        -autorecon3

                          cheers
                          Bruce


                          On Tue, 31 Jul 2012, Peter McNally
        wrote:

                                Dear FreeSurfer Experts,

                                I am using Freesurfer
        version 5.1 over
                    at the
                                University of Pennsylvania,
                                and I have been running into
        issues with
                    the optic
                                chiasm. Despite having
                                edited it out on both the
        brainmask.mgz
                    and wm.mgz
                                volumes, FreeSurfer has
                                been insisting that it be
        included as a
                    surface on
                                multiple participants.
                                Does anyone know a way to
        resolve this?
                    Thank you
                                very much for your time.

                                Best,
                                Peter McNally


                                PS: I have included an
        example as an
                    attachment
                                (.pdf)






                    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.