Hi Daniel the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce On Tue, 19 Apr 2016, dgw wrote: > Here is the log for the most recent -autorecon2-wm call: > > Thanks! > d > > On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu> wrote: >> can you send us the recon-all.log? I don't see an obvious reason why it >> wouldn't have worked >> On Tue, 19 Apr 2016, dgw wrote: >> >>> Just to follow up, I have tried several different options with >>> recon-all to get the white matter edits to stick on this participant, >>> and it doesn't seem to be working: >>> >>> re-editing wm.mgz and running recon-all -autorecon2-wm >>> re-editing wm.mgz and running recon-all -make all >>> >>> I can't seem to get any appreciable change in the white matter >>> surface. I have attached a screenshot, for an example. >>> >>> hth >>> d >>> >>> >>> On Mon, Apr 18, 2016 at 10:30 AM, dgw <dgwake...@gmail.com> wrote: >>>> Hi, >>>> >>>> I recently edited a brain with a gyral cyst, carefully filling the >>>> cyst with white matter in the wm.mgz. Unfortunately after running: >>>> /usr/local/freesurfer/stable5_3_0/bin/recon-all >>>> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 >>>> >>>> none of the edits were incorporated. >>>> >>>> Is the FLAIRpial flag incompatible with autorecon2-wm? >>>> >>>> Is there some other misake? >>>> >>>> I followed this guide >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview >>>> >>>> Thanks, >>>> Dan >>> >> _______________________________________________ >> 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
