Hi Daniel I'm out if town , can you remind me next week? This is fixed in v6 I think if you want to just run the pial stuff in it Bruce
> On Apr 21, 2016, at 10:41 AM, dgw <dgwake...@gmail.com> wrote: > > Hi, > > I followed the advice, and the White Matter surface looks much better; > however, now the pial surface is crossing the white matter surface. > > I ran the following: > /usr/local/freesurfer/stable5_3_0/bin/recon-all > -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8 > > for those at Martinos the new subjid should indicate the new path. > > I've attached a screenshot. Thank you in advance for any advice you can give. > > Thank You, > Dan > >> On Tue, Apr 19, 2016 at 5:29 PM, dgw <dgwake...@gmail.com> wrote: >> Hi Bruce, >> >> Thanks! I'll give it a whirl. >> >> d >> >> On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >>> 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 > <pial_surface.png> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
