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 correct 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 aseg.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 how 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_64 x86_64 x86_64 GNU/Linux
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