Hi Marie
hmmm, it's hard to see without seeing why it is happening. Maybe you can
attach some images? Alternatively you can upload a subject dir and give
us the coordinates of the regions that are not as accurate as you would
wish, and we will take a look.
cheers
Bruce
On Wed, 7 Mar 2018, Marie Sigmund wrote:
>
> Hello FreeSurfer Developers,
>
> I am trouble-shooting some FreeSurfer Data and there are two errors which occur frequently.
>
> 1. The pial surface does not include all of the graymatter. I read that you should in this case corr
> ect the WM so it adjusts the GM automatically. I tried this out a couple of times and there is still
> some GM left over which is not included.
>
> 2. Gyri or sulci are sometimes labeled as wm-hypointensities. I thought about correcting it on the a
> seg.presurf volume (on the website it is stated that using a FreeSurfer version of 6.0 or higher you
> should make corrections to the ASEG there). The problem is that on this volume the segmentation is
> different to the final one and not necessarily wrong.
>
> I've searched the list and no similar errors have been reported. Does anyone have any thoughts on ho
> w to trouble-shoot this one? Thanks a lot!
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 2) uname -a: Linux R0223 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_6
> 4 x86_64 x86_64 GNU/Linux
>
>
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