I'll leave the first question for Bruce or Jenni. The 2nd depends on
what you are going to do with the talairach. If you are not going to be
reporting talairach coords, then you can be quite sloppy as they are
only used to create seed points for more-or-less finding the CC, pons,
etc. If you are going to report talairach coords, then you only need to
align the outside of the brain to the mni305. There is no perfect
talairach reg, and in the best case it's going to be pretty awful:). If
you get it within a centimeter, you're probably ok.
doug
Paul Greenberg wrote:
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
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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