Hello everybody,

I am gladly starting my freesurfer adventure after the awesome last course in Copenhagen, but I have quickly realized that troubleshooting on your own is not as easy as with experts going around in a room.

I was looking for errors after having run the recon all and I stumbled upon this crossing between white and pial surface in the lingual gyrus (see attached Figure1, green arrow).

It seems to me that the problem may arise from the fact that in the WM volume (see attached Figure2) there are areas that have been categorized as WM hypointensities, and in particular on the right, the problem could be that the white matter surface, instead of going around these brighter voxels, just goes straight down (I hope I have explained myself). Is the fixing to this problem changing the value of those voxels (part of them, of course) in the WM volume ?  If I look at the WM seg I see that indeed they are left out from the mask. Or should I do something else ?

I am working with freesurfer version Linux-centos6_x86_64-stable-pub-v5.3.0, with Linux version 3.10.0-327.4.5.el7.x86_64 (Red Hat 4.8.3-9).

Thanks in advance for any suggestion

Alain