Looking at the image posted previously.....
https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
I think it is pretty clear the 5.1 picture has better gray/white contrast. It is a very subtle difference, but you can see it if you look at some pieces of wm that were "missed" by 5.2 in this image.
On Thu, Apr 11, 2013 at 12:33 PM, Yang, Daniel yung-jui.yang@yale.eduwrote:
Thanks Nick! I have uploaded the relevant files to you.
Thanks, Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 4/10/13 1:19 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Daniel,
We're repeating our paired-analysis of thickness measures between 5.1 and 5.2. In the meantime, to check for correctness, open the brain.finalsurfs.mgz file with the surfaces overlayed, and check the intensity value of the voxels which appear to be non-cortical 'black spaces', relative to neighboring gm voxels. ignore the aseg.mgz gm voxels, as those are not accurate (ie, dont load aseg.mgz when inspecting surfaces, or at least turn if off when inspecting gm regions....its still handy to see where hippocampus sits).
Nick
On Wed, 2013-04-10 at 11:11 +0000, Yang, Daniel wrote:
Dear FreeSurfer Experts and Users,
Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical "black spaces" within pial surfaces, compared to FS 5.1?
I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten.
At the meantime I keep receiving Emails from people asking me this issue.
Thanks! Daniel
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