Dear Experts,
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.
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.
Thanks.
Mo
PS I can post screen
