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.eduwrote:
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<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.