Hi All,

I am currently running freesurfer on a group of subjects, some of which have some bright areas of GM near the surface of the pial line that is getting included as WM. As per the wiki article here I erased the offending GM from the wm.mgz file, and reran with the command:

recon-all -autorecon2-wm -autorecon3 -subjid SUBID

However, despite making the edits and rerunning, the ?h.white surfaces did not seem to adjust to the revised wm.mgz file (in fact, they looked pretty much the same as before). I found an exchange on the listerv here, where it was suggested that Max look at the ?h.orig.nofix files, to see if the changes were recorded there. I opened the ?h.orig.nofix (yellow) up next to the ?h.white file (red), and you can see those in the attached image wmedits.png. An image with the edited wm.mgz file as a heat overlay is included (wmeditswithwm.png)

I could see that the edits made to wm.mgz are being saved/read/interpreted correctly, and the nofix file was being saved correctly, but it doesn't seem to be influencing the surface file correctly.

Do you have any idea what might be going on here?

Thanks very much for any help you can provide,

Andrew