3D deformation

[Brent Womble]

Hi all,

I'm trying to test the accuracy of our lab's longitudinal structural
pipelines (FreeSurfer and SPM12, specifically). To do that, I want to make
some fake longitudinal structural data. I want to take 20 real
pre-treatment T1's and manually stretch the cortex in our ROI (primary
motor cortex) to make fake post-treatment scans. Then I'll run the
synthetic data through our longitudinal pipelines and compare the results.

I've figured out how to do this in 2 dimensions using the interactive
moving least squares tool in ImageJ (using an affine deformation). However
all of the deformation tools in ImageJ are 2D, so they only change that one
slice. I need to find a way to change that slice and a few adjacent slices
- tapering the deformation so it blends in with rest of the 3D image.

One way to do this in ImageJ would be to:

   1. Save the transform grid from the interactive moving least squares tool
   2. Use some software to calculate transform grids that fall-off in a
   Gaussian distribution towards a non-transformed grid, within a certain
   number of slices.
   3. Apply the full set of transformation grids to the stack (the target
   slice and several adjacent slices).

I don't know very much Java, so actually implementing this would be a
challenge.

Is there another tool that I could use to create and apply a 3D deformation
to a single T1 image?

Thanks,
-Brent Womble

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