Ok perfect. Just one last question, how would I use the thresholded option for the annotations (i.e. aparc.DKTatlas40.annot, aparc2009s.annot) when doing whole brain analyses?

Thanks!


On Sun, Nov 17, 2013 at 1:20 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
for most purposes, yes

Bruce
On Sun, 17 Nov 2013, krista kelly wrote:

Great thanks Bruce! I'm assuming then that using the thresh.label is the
best choice.


On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Krista

      the unthresholded labels give every point that has a non-zero
      probability of being in the label, no matter how unlikely. The
      .thresh ones are thresholded to pick the most likely vertices
      that give a label that is the right surface area.

      cheers
      Bruce
      On Sun, 17 Nov 2013, krista kelly wrote:

            Hi, I've just started using the newest freesurfer v
            5.3 and I've noticed in
            the labels folder that every .label has a
            thresh.label. When overlaying the
            two, they can be quite different (for example
            MT.label is much larger than
            MT.thresh.label) or quite similar (V1.label is just
            a tiny bit larger than
            V1.thresh.label). What is the difference between the
            two and which is best
            to use?
            Thanks!
            Krista




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