Bruce, Main problem area that I can see is at coordinates [104,42,124].
My first attempt, I don't think I had the recon editing box checked when I was editing the white matter, but I used a brush value of 255. My second attempt I painted over the same voxels but with the recon editing box checked. Both times, after saving wm.mgz I ran the following command: "recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd`" Only thing different from the guide is I specify a different subject directory. Below are download links for the important files, let me know if you would like to look at anything else. If you look at wm.mgz along with the rh.white, you can see the surface doesn't appear to acknowledge my edit. 001.mgz: https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc recon-all.logs.tar.gz: https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji brainmask+surf+wm.tar.gz https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3 Thanks tremendously for your time, Eli > ------------------------------ > > Message: 4 > Date: Wed, 1 Mar 2017 16:39:33 -0500 (EST) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] wm.mgz manual editing > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alpine.LRH.2.20.1703011638420.14038-40door.nmr.mgh.harvard.edu&d=DwICAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=yBgXIybzSgTt6ZfKp6pNzp_N8aWytMgQmmsZVDx1AwI&s=BM5wWGqXMNLiptKsXqsKDinkU3EtRMoCYFuj0Gbx650&e= > > > Content-Type: text/plain; charset="utf-8" > > Hi Eli > > hmm, maybe you should just upload the subject and email us the voxel > coords you are talking about? > > Also, in general it is hard for us to help you unless you include more > information. What exact command did you run? What was the screen output? > What was in the recon-all.log? > > cheers > Bruce > > > On Wed, 1 > Mar 2017, Rockers, Elijah D. wrote: > > > Couple of questions: > > > > 1) > > > > I edited wm.mgz following the instructions in the wiki guide, but it did > > not change anything after reconstruction. I am still using 5.3 right > > now, so maybe the guide is wrong for me. What is the brush value > > supposed to be? I used 255 but it did not extend the white matter > > surface to include my edits. I checked to make sure they saved > > correctly, they did, but the surface didn't change. Any ideas? > > > > 2) > > > > The reason I am editing wm.mgz is to try to include some cortex that was > > left out of the pial surface. I don't suppose there's any way to fix > > this without editing wm.mgz? Because the white matter surface actually > > looks fine the way it is. > > > > Thanks, > > Eli > > > > Houston Methodist. Leading Medicine. > > Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. _______________________________________________ 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.
