Dear Experts, <br><br>I am a beginner to the use of Freesurfer and 
having just installed version 5.1.0 (Centos 64bit) I have been going 
through the processing pipeline with one of our own datasets (3T GE 
Excite II scanner - coronal T1-weighted volumetric acquisition sequence 
with 1.1-mm thick slices).  recon-all works fine and I have been looking
 at the outputs.<br>
<br>I have a question regarding the subcortical segmentation especially 
around the basal ganglia - during the intensity normalisation it appears
 to have assigned similar high (110) voxel values to parts of the internal capsule,
 pallidum and thalamus (pic1- brainmask.mgz), though the actual 
segmentation (pic2-aseg) looks reasonable when compared with the 
native image (pic3-raw T1) (though I appreciate one is normalised 
and the other is not).  Should I be worried about this (and if so how 
can I correct ?) or is this intensity normalisation used only in the 
surface stream with a different intensity normalisation used in the 
volume stream ?  Or ... is it used in the volume stream but the other 
parts of the model (eg priors from atlas etc) compensate in some way.<br>
<br>Thanks.<br><br>Mo<br><br>PS I can post screen<br>