Hi Andrew
can you tell us more about the acquisition? Is it 3T? 1.5? Did you use
any special options to recon-all (like the 3T one or the mprage one)? It's
really tough to tell from just an image of a single slice. If you upload
the dataset we can take a look
cheers
Bruce
On
Mon, 17 Nov 2014, O'Shea,Andrew wrote:
Hello all,
I have heard about the issue of inaccuracy in the temporal lobes but never
had problems myself until I recently tried processing a dataset from an
outside group. On this data, the pial boundary are severely underestimated
in the temporal lobes. It is worse right when the temporal lobes are coming
into view as you slice back from the front of the brain along the coronal
plane. I have attached a screenshot to show what I mean. Basically sections
of the medial temporal lobe (greater than the hippocampus/amygdala area) and
lateral temporal lobe are not included in the surfaces. The GM/WM contrast
does not look very prominent in the t1 images.
Is there any options we can specify which will lower the needed manual
edits. I tried the ‘-mprage’ flag but that didn’t seem to help. Right now we
have tried adding lots of control points but that doesn’t fix the issue
100%.
Thanks for the help!
-Andrew
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