Hi Alain
I'm pretty sure that this is a bug in 5.3 that is fixed in dev and will
not be an issue in 6.0. You can test this by downloading and trying out
dev if you like.
cheers
Bruce
On Fri, 9 Sep 2016, Alain Imaging wrote:
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
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