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
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