[Insight-users] Deformable transform

[Ganesh Narayanasamy]

Thanks for your suggestions. I have been using 3D-Slicer for viewing the images.
What I would like to do is use diffeomorphic demons algorithm developed by Vercauteren T et al. (http://www.insight-journal.org/browse/publication/154) to register a pair of image volumes and apply the resulting deformation onto a 3rd image volume.
The command used for registering images I1, I2 is:

>DemonsRegistration.exe -f I1.mha -m I2.mha -o OutputI1I2.mha -a 1 -l 0.5 -s 0.8 -i 50x50x50 -d 1

This command generates these output files:
 WarpedGridImage.mha
 TransformJacobianDeteminant.mha
 OutputI1I2.mha
 ForwardWarpedGridImage.mha
 and
 metricvalues.xls

I can see that WarpedGridImage.mha is the deformation warping grid, but which one of these files is the deformation field ? Is there a way to convert these output mha files into tif format as 3D-Slicer cannot convert some of them?

As stated above, I would like to apply the resulting deformation onto a 3rd image volume, say, I3 and this can be done using WarpImageFilter1.exe. Should the command be like:

> WarpImageFilter1 I3.mha WarpedGridImage.mha Final.mha

Thank you,
Ganesh

************************************************************************

"What the mind of man can conceive and believe, It can achieve" - Napolean Hill

-Ganesh 
Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center

Earlier work: 
http://www.sciencedaily.com/releases/2007/05/070504133017.htm

************************************************************************
 
> Message: 2
> Date: Thu, 15 Apr 2010 21:36:36 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: Re: [Insight-users] Deformable transform
> To: Ganesh Narayanasamy <nganesh76 at hotmail.com>
> Cc: insight-users at itk.org
> Message-ID:
> 	<g2gf7abd23c1004151836n31198261ze51659653f880167 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Ganesh,
> 
> You may want to use the
> 
> http://www.itk.org/Doxygen/html/classitk_1_1WarpImageFilter.html
> 
> You may also find useful the "vv" application:
> 
>                    http://www.creatis.insa-lyon.fr/rio/vv
> 
> It provides functionalities for visualizing the outcome of deformable
> registration, including the overlapping of the deformation field.
> 
> 
>     Regards,
> 
> 
>           Luis
> 
> 
> ------------------------------------------------------------------
> On Mon, Apr 12, 2010 at 5:17 PM, Ganesh Narayanasamy
> <nganesh76 at hotmail.com>wrote:
> 
> >
> > We have 2 sets of 3D-CT data, one from radiotherapy planning CT (call it as
> > image I1) and another one is a cone-beam CT on the treatment table (image
> > I2). Performing a deformable registration on these gives us a deformation
> > field, say DF.
> > I would like to see how the individual structures have deformed between
> > image I1 and image I2. The structure that we are interested in (say, S1) is
> > masked from image I1 and DF should be applied on it. We would like to see
> > how this structure has deformed in the image I2 (its new form is called say,
> > S2).
> > Error = || DF(S1) - S2 ||
> >
> > Can you help me in applying DF onto S1. Probably for a few out there, this
> > is probably trivial. Should I write a new set of code or is there something
> > that is already available?
> >
> > Thanks,
> > Ganesh
> >

 		 	   		  
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