and the papers describing the subcortical segmentation scheme are found at the bottom of the main wiki page:
http://surfer.nmr.mgh.harvard.edu/fswiki
in the section 'subcortical segmentation'.
On Tue, 2007-11-13 at 15:17 -0500, Doug Greve wrote:
Look in $FREESURFER_HOME/FreeSurferColorLUT.txt
doug
joel bruss wrote:
This is the last question that I have...sorry to keep bothering you all. Is there a page on the FS wiki or is there a man page that details the value of each sub-cortical parcel? I see that each masked are has a value (1, 2, 3, etc.) but before I make assumptions about which values correspond with which region, I though I'd ask for help.
-Joel
On Nov 13, 2007 1:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Joel,
both the .m3z (nonlinear) and the .lta (linear) are transforms from the subject to the atlas coordinate system, but all the labeling is done in the subject space, so you should be set.
cheers, Bruce On Tue, 13 Nov 2007, joel bruss wrote:
Hello-
I'm running FreeSurfer v4.01on SUSE Linux
I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but in the native MRI space. I see that the output of "CA Label" produces a file that is fit to the "CA Normalize" step but I can't figure out the transform that was used. Specifically, for CA Normalize, if I look under /mri/transforms, and sort by time, I have both the talairach.lta and talairach.m3z files, but neither will get me from native to norm space (or vice-versa). Is there a transform file that I'm missing or is this a process of intermediate steps to get from native to norm space? Please help!
Thanks, Joel
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