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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
