[Mristudio-users] LDDMM Kimap problems

[susumu mori]

Hi Chase,

We'll keep our eyes on reports from other users. If this is an isolated
case, I suspect there is a procedural error.
Please check Template and Target images that were included in the returned
results.
Make sure that these images are what you meant (Template = atlas, Target =
your image).
Maybe these two images are identical (thus no transformation) for some
reason.

Also, please check the text files in the results and make sure your alpha
values were really 0.01, 0.005, 0.002.

Susumu

On Sat, Dec 8, 2012 at 7:35 PM, Chase Figley <cfigley at gmail.com> wrote:

> 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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