Hello,
I've got a question about cortical surfaces in the ventral regions below the basal ganglia and about tkregister output quality control.
I'm using the latest version of freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5
1) In the majority of my data sets, white matter surfaces near the basal ganglia rise dorsally to include large volumes of the basal ganglia (putamen, nucleus accumbens, both hemispheres) - attached image. This results in inaccurate cortical volumes and thickness estimates from the surface based data for these regions. How can I compensate for these surface problems in order to get the best possible estimate of total cortical volume? I've tried editing the white matter manually and this has little effect on the locations of white matter surfaces in the basal ganglia.
2) I'm having a difficult time knowing how to determine if the talairach registration is good enough for each data set, and judging the quality of my manual edits using tkregister. Could you post an additional series of tiff or jpg images (multiple parasagittal, coronal, horizontal) showing how cortical surfaces and movable volumes are supposed to align in each plane? It would help to see examples of registrations that are "perfect", "good enough not to edit", and "bad enough to require adjustment".
Thanks very much!,
Paul