Hi Brent
are you saying you just multiplied the gray matter intensities by some
scale factor (>1)?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Hi everyone,
I've been making synthetic brains to test how Freesurfer handles various
structural changes.
One of the changes I'm testing is increased density (like in VBM). To
simulate increased density, I used a spherical Gaussian multiplication
kernel, with a radius of 20 voxels. I centered this kernel at a point in
the right superior frontal gyrus and masked the changes to grey matter using
the segmentation output from SPM12.
Here is an example, a difference image (synth.nii - pre.nii):
[IMAGE]
Around that area, Freesurfer didn't detect a change (as I expected):
Inline image 2
Original in red and blue, synthetic in pink and light blue.
The problem is that the longitudinal streams in Freesurfer found a bunch of
changes in random parts of the brain.
We looked at the recons for each subject individually, and saw some noise
around the clusters that were significant in the two-stage model. This
doesn't make sense, because the actual voxels were exactly the same in that
region. For example:
[IMAGE]
I redid the recon-all with the -nonormalization flag. It didn't fix the
problem. For example (same subject as above):
[IMAGE]
I thought it might have been an issue caused by my increased density method,
so I ran it again, this time with the kernel centered in the cerebellum
(still masked to grey matter). I still got weird changes in unrelated parts
of the cortex. For example (same subject as above):
[IMAGE]
Note: light blue/red and blue/red are reversed in this one, just because of
the order I loaded it in Freeview.
In summary, Freesurfer found a bunch of weird changes that were nowhere near
the changes I actually made.
Where should I go from here?
-Brent
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