Dear Bruce, no, both ?h.orig.nofix and ?h.orig are ok (respecting my wm.mgz edits), but only ?h.white (result of mris_make_surfaces) is not ok (leaking to regions where wm.mgz has value 1).
Regards, Antonin > Hi Antonin > if it is correct in the orig.nofix but not correct in the orig that means > it was an incorrectly fixed topological defect that you need to manually > correct. I'll see if we can find someone here to take a look. > Bruce On Wed, 29 Jul 2015, Antonin Skoch wrote: > Dear experts, > > during the manual correction of freesurfer reconstruction I encountered > following > problem: > > White surface did not follow gray / white matter boundary probably partly due > to > skullstrip error and partly to the insufficient local gray/white matter > contrast. > I tried to fix it by editing wm.mgz, in some cases it worked well, but in > some > cases white surface "does not respect" my wm.mgz editing and still leaks out > to > the areas where wm.mgz has value 1. > The problem is probably at the level of recon-all -white since orig.nofix.mgz > and > orig.mgz are OK - does well follow my edits and does not leak to areas with > wm.mgz = 1. > I tried to put some control points to these areas but it still did not help > (the > brainmask.mgz at most of the problematic areas has intensity 110). Processing > the > data by development version did not help either.? > > I have uploaded 2 examples to your ftp file exchange: > > not_corrected_wm_1 > - slice 96 in coronal view, right hemisphere, at the convexity > - slices 97-98, 103, 107,108, in coronal view,? left hemisphere, at the > convexity > > not_corrected_wm_2 > - slices 78 in coronal view, right hemisphere, 2 areas at the convexity > - slices 79-83 in coronal view, two quite large areas in both hemispheres at > the > convexity > - slices 88-95 in coronal view, quite large areas at righ hemispheres at the > convexity > > and other areas in following slices, there are quite large amount of them in > this > subject. > > Could you please look at the data to find where could be the problem? > > Thank you very much for all your help. > > Best regards, > > Antonin Skoch > >
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