Dear FreeSurfer Developers,
We are attempting to make manual white matter edits to our subjects. The edits are saving; however, after running with recon-all, the WM surface does not appear to be taking into account our edits made to wm.mgz. Below is additional information, and I have attached our recon-all.log. We are only editing the cross because our dataset is comprised of single timepoints.
We are using FreeSurfer v5.3 and our operating system is OS X El Capitan version 10.11.6.
Command to open and edit WM:
freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red
Command to submit edits:
recon-all -autorecon2-wm -autorecon3 -subjid
Recon-all log (see attached)
Thank you,
Kaley Ellis
Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison