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)






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