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.

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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