[Mristudio-users] LDDMM Kimap problems

[Chase Figley]

Hi LDDMM and DiffeoMap Experts,

I have uploaded a few datasets to the LDDMM server over the past week and
have successfully retried my results.  However, when I apply the Kimap.vtk
to my linearly normalized AIR images (skull stripped mean b0), I don't see
any changes in my updated "lddmm" images.  And similarly, when I combine my
AIR and Kimap.vtk files to generate an "OverallKimap", the images come out
looking the same as the linearly normalized AIR images.

This is particularly obvious in some of my older subjects who have large
ventricles.  While the outer dimensions of their brains look fine, the
subcortical structures are clearly not properly aligned, so this leads me
to believe that there is something wrong with my Kimap.vtk files.

Does anyone know what might be happening here (and/or have any
recommendations)?  Has anyone else had a problem like this lately?

In case it matters, I have tried to use all of the default settings, except
I used the three-step elasticity option (alpha = 0.01, 0.005, 0.002).
However, I am a Mac user who has been doing things through a virtual
machine, and since DiffeoMap will not create the process.md5 file
correctly, I have been doing the last few steps (i.e., creating the md5sum,
and uploading to the server through the Terminal).  I thought everything
would have worked fine because I was able to upload and download my data,
but could this be causing any problems?

Thanks in advance for any help/advice,

Chase

-- 
Chase Figley, PhD
Johns Hopkins University
Department of Neuroscience
Department of Psychological and Brain Sciences
F.M. Kirby Research Center for Functional Brain Imaging
http://sites.google.com/site/cfigley/
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