[Insight-users] Re: [Fwd: MultiResMIRegistration]

[Luis Ibanez]

Hi Christos,

ITK is N-Dimensional.

The registration metrics can manage 2D, 3D, 4D,...

The limit is only the memory of your computer
and the amount of time that you want to let it
running.

For 3D registration you can use as Transform:

  -Rigid 3D,
  -Affine 3D
  -Deformable registrations.
       - BSplines
       - Demons
       - FEM

You could try directly the FEM based registration
since you can setup MutualInformation as the metric.

Please look at the registration chapter in the
SoftwareGuide


     http://www.itk.org/ItkSoftwareGuide.pdf

Both to the basic registration framework and to the
deformable registration section.


Regards,



    Luis


---------------------------
Christos Panagiotou wrote:

> dear luis
> 
> sorry for the direct contact but i saw in the itk mailing list archive 
> that you were involved in a thread about
> MultiResMIRegistration and i thought you might be able to help me with 
> the following problem
> 
> hopefuly it will be something very simple and will not take much of your 
> time
> thank you very much in advance
> 
> christos
> 
> p.s. i have one additional question to ask you if it is possible
> is the implemented algorithm applied directly to the 3D matrices of the 
> volumes or does it implement the alignment
> slice by slice? i am asking you this because ultimately i want to 
> implement a _non-rigid _registration of 3D volumes where the alignment 
> is made by direct 3D transformations. The non-rigid transformation will 
> be implemented by a technique suggested
> by DR. D. Rueckert and uses Free Form Deformations implemented with 
> B-Splines. To do this i need first to align the images using the Viola 
> MI technique which ITK has already implemented. The only thing i need to 
> know if it makes direct 3D transformations or if it is reslicing the 
> volumes and apply the MI alignment slice by slice...
> 
> thank you very much for your time
> 
> -------- Original Message --------
> Subject: 	MultiResMIRegistration
> Date: 	Mon, 16 Feb 2004 02:41:05 +0000
> From: 	Christos Panagiotou <cpanagio at cs.ucl.ac.uk>
> To: 	1__ITK POST <insight-users at itk.org>
> 
> 
> 
> guys
> 
> i have a problem testing the MultiResMIRegistration
> 
> I have some raw volumes stored in single files ( i downloaded also a 
> sample from http://www.bic.mni.mcgill.ca/brainweb/selection_normal.html 
> as suggested)
> 
> I run the application and i get the following error messages:
> 
> -------------------------------ERROR----------------------------------
> 
> ./MultiResMIRegistration ~/PhD/Data/raw/test.txt
> Parsing input ...
> Fixed image filename: 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> Big Endian: 0
> Image Size: [181, 217, 181]
> Image Spacing: [1, 1, 1]Moving image filename: 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> Big Endian: 0
> Image Size: [181, 217, 181]
> Image Spacing: [1, 1, 1]Permute order: [0, 1, 2]Flip axes: [0, 0, 
> 0]Number of levels: 5
> Fixed image shrink factors: [4, 4, 1]Moving image shrink factors: [8, 8, 
> 1]Number of iterations: [2500, 2500, 2500, 2500, 2500]Learning rates: 
> [1e-04, 1e-05, 5e-06, 1e-06, 5e-07]Translation scale: 320
> PGM directory: /home/christos/PhD/Data/raw/pgm
> 
> Error while reading in fixed image.
> Error occured during registration
> itk::ExceptionObject caught
> 
> itk::ImageFileReaderException (0x9470288)
> Location: "Unknown"
> File: /home/christos/Applications/ITK/Code/IO/itkImageFileReader.txx
> Line: 101
> Description:  Could not create IO object for file 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> 
> 
> Caught an ITK exception:
> 
> itk::ImageFileReaderException (0x9470288)
> Location: "Unknown"
> File: /home/christos/Applications/ITK/Code/IO/itkImageFileReader.txx
> Line: 101
> Description:  Could not create IO object for file 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> 
> -------------------------------ERROR----------------------------------
> 
> the input file is just an alteration of the sample inputs where i 
> altered the paths and some other info s.a. volume xyz sizes, the pgm 
> output dir etc.
> 
> i also paste the input file incase i did something wrong there and i 
> cant see it...
> 
> --------------------------------input--------------------------------------
> 
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> 0
> 181 217 181
> 1.0 1.0 1.0
> /home/christos/PhD/Data/raw/pd_icbm_normal_1mm_pn0_rf0.raws
> 0
> 181 217 181
> 1.0 1.0 1.0
> 0 1 2
> 0 0 0
> 5
> 4 4 1
> 8 8 1
> 2500 2500 2500 2500 2500
> 1e-4 1e-5 5e-6 1e-6 5e-7
> 320
> /home/christos/PhD/Data/raw/pgm
> 
> --------------------------------input--------------------------------------
> 
> as you see i am using the same volume however i tried also with 
> different volumes from the brainweb and alternate sources...
> 
> any suggestions would be appreciated
> 
> thanks
> christos
> 
> 
> -- 
> ---------------------------------------------------
> 
>  Christos Panagiotou
> 
>  PhD student
>  University College London
>  Dept. of Computer Science
> 
>  Tel 1: +44 (0)20 7679 3462 (Direct Dial)
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>  Fax: +44 (0)20 7387 1397
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> 
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