Hi Paul,
I would have said you'll need to edit the wm, but you say you've tried.
Could you send along a shot of that same exact slice but on the wm.mgz
volume?
thanks,
Jenni
On Mon, 26 Mar 2007, Doug Greve wrote:
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
------------------------------------------------------------------------
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
