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 dgwakeman@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_freevi...
Thanks, Dan