Hi Andrew What does the ?h.orig look like? And what is the intensity volume in the background? Cheers Bruce
> On Jul 14, 2014, at 4:18 PM, Andrew Schoen <schoen.andr...@gmail.com> wrote: > > 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 > <wmedits.png> > <wmeditswithwm.png> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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