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multimodality non-rigid demon algorithm image registration

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multimodality non-rigid demon algorithm image registration

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16 Sep 2008 (Updated )

non-rigid 2D and 3D image registration with demon (fluid) algorithm, extended with modality transf.

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Description

This function will perform demon registration which is an type of fast non-rigid fluid like registration between two 2D or 3D images. Registration between different (MRI) modalities is also supported, through a function which transform one image modality so it looks likes the modality of the second image.

The demon registration is described by the paper of Thirion 1998 and extended by Cachier 1999 and He Wang 2005.

Basic algorithm: On each pixel a velocity (movement) is defined with use of the intensity differences and gradient information. This velocity field is smoothed by an Gaussian, and iteratively used to transform the moving image, and register on to the static image. (Easy to understand code example in file basic_demon_example.m)

Instead of using the basic equations for the "demonregistration" function, we have rewritten it to be used by an limit memory BFGS optimizer in an iterative and multi-resolution way, with also support of diffusion regularization. (see also Tom Vercauteren et al. "Non-parametric Diffeomorphic Image..." )

Transforming one modality into the fake modality of the other image is done with use of 2D mutual histograms between regions of both images, and choosing the grey values which have the highest correlation. D. Kroon et al. "MRI Modality Transformation in Demon Registration" (MutualTransform.m)

See the screenshot for an example result.

Usage:
The functions register_images.m and register_volumes.m are easy to use, and will fit most applications.
First compile the c-code : compile_c_files.m.

Notes:
- All the mex-code is multi-threaded and is tested on both Windows and Linux.
- Please leave comments and report bugs

Required Products Image Processing Toolbox
MATLAB release MATLAB 7.6 (R2008a)
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Comments and Ratings (63)
21 Aug 2014 Michael

Problem below solved:
It turns out the problem was that I had first downloaded the packages on a Mac and then copied them onto the Windows machine. Somewhere along the line, hidden files (with the prefix ._) with the .c extension were added to the folders by the Mac, and the windows compiler was trying unsuccessfully to read them. When I redownloaded the packages on the windows machine, everything was good.

20 Aug 2014 Michael

Hi I am having trouble running the compile c files on a Windows 7 computers.

The error I get is the following

compiling : ._bspline_error_2d_double.c -> Default options filename found in C:\Users\Orger\AppData\Roaming\MathWorks\MATLAB\R2012a ---------------------------------------------------------------- -> Options file = C:\Users\Orger\AppData\Roaming\MathWorks\MATLAB\R2012a\mexopts.bat MATLAB = C:\Program Files\MATLAB\R2012a -> COMPILER = cl -> Compiler flags: COMPFLAGS = /c /GR /W3 /EHs /D_CRT_SECURE_NO_DEPRECATE /D_SCL_SECURE_NO_DEPRECATE /D_SECURE_SCL=0 /DMATLAB_MEX_FILE /nologo /MD OPTIMFLAGS = /O2 /Oy- /DNDEBUG DEBUGFLAGS = /Z7 arguments = Name switch = /Fo -> Pre-linking commands = -> LINKER = link -> Link directives: LINKFLAGS = /dll /export:mexFunction /LIBPATH:"C:\Program Files\MATLAB\R2012a\extern\lib\win64\microsoft" libmx.lib libmex.lib libmat.lib /MACHINE:X64 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /manifest /incremental:NO /implib:"C:\Users\Orger\AppData\Local\Temp\mex_1feKKo\templib.x" /MAP:"_bspline_error_2d_double.mexw64.map" LINKDEBUGFLAGS = /debug /PDB:"_bspline_error_2d_double.mexw64.pdb" LINKFLAGSPOST = Name directive = /out:"_bspline_error_2d_double.mexw64" File link directive = Lib. link directive = Rsp file indicator = @ -> Resource Compiler = rc /fo "mexversion.res" -> Resource Linker = ----------------------------------------------------------------

--> cl /c /GR /W3 /EHs /D_CRT_SECURE_NO_DEPRECATE /D_SCL_SECURE_NO_DEPRECATE /D_SECURE_SCL=0 /DMATLAB_MEX_FILE /nologo /MD /FoC:\Users\Orger\AppData\Local\Temp\mex_1feKKo\.obj -I"C:\Program Files\MATLAB\R2012a\extern\include" /O2 /Oy- /DNDEBUG -DMX_COMPAT_32 ._bspline_error_2d_double.c

._bspline_error_2d_double.c ._bspline_error_2d_double.c : warning C4821: Unable to determine Unicode encoding type, please save the file with signature (BOM) ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x5' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x16' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x7' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x2' ._bspline_error_2d_double.c(1) : error C2061: syntax error : identifier 'OS' ._bspline_error_2d_double.c(1) : error C2059: syntax error : ';' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x2' ._bspline_error_2d_double.c(1) : error C2143: syntax error : missing '{' before 'constant' ._bspline_error_2d_double.c(1) : error C2059: syntax error : '<Unknown>' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0xe' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x2' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0xe' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1e' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0xe' ._bspline_error_2d_double.c(1) : error C2061: syntax error : identifier 'É~9' ._bspline_error_2d_double.c(1) : error C2059: syntax error : ';' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x15' ._bspline_error_2d_double.c(1) : error C2061: syntax error : identifier 'com' ._bspline_error_2d_double.c(1) : error C2059: syntax error : ';' ._bspline_error_2d_double.c(1) : error C2059: syntax error : '.' ._bspline_error_2d_double.c(1) : error C2021: expected exponent value, not 'b' ._bspline_error_2d_double.c(1) : error C2059: syntax error : 'bad suffix on number' ._bspline_error_2d_double.c(1) : error C2059: syntax error : 'constant' ._bspline_error_2d_double.c(1) : error C2143: syntax error : missing '{' before '-' ._bspline_error_2d_double.c(1) : error C2059: syntax error : '-' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1e' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1e' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1c' ._bspline_error_2d_double.c(1) : error C2018: unknown character '0x1e'

C:\PROGRA~1\MATLAB\R2012A\BIN\MEX.PL: Error: Compile of '._bspline_error_2d_double.c' failed.
I have tried using Matlab R2012A with Microsoft SDK as the compiler, and I also tried on another computer R2010A using Visual C++ 2010 Express and got the same error. I also tried adding a BOM to the file bspline_error_2d_double.c which didn't seem to fix the problem (maybe it is another file that needs a BOM?).

Thank you to anyone who can help. This is quite frustrating, and I have not been able to find anyone with a similar problem by googling.

21 Aug 2013 Andy A

Thanks, generally works well but there seems to be a problem with the shear components. I made the change suggested by Ryan Wu in my copy of register_images.m and this seems to fix it.

(M=make_transformation_matrix(x(1:2),x(3),x(4:5),x(6:7));

17 May 2013 PDraper

The 3D registration doesn't work for me with sample 250x250x200 images... any reason why? This would be a fantastic aid otherwise.

22 Aug 2012 henry wang

To clarify, got this working for 2D, but for 3D modifying affine_error_3d_double.c but it doesn't work for 3D case.

I have 2 images, IM1, IM2. IM2 is a filled with value of 70s over a ROI and 0s elsewhere. I want to register IM1 with IM2 such that the MSE is minimized over the region where IM2 has value of 70s. Using rigid transformation.
Is this possible to do? This is not a direct image registration problem because IM1 and IM2 are not really same image. I want to find transformation such that sum(IM2(T*x)-IM1(x))^2 is minimized where IM2(T*x)=70. I tried to modify squared_difference_double.c:
if (I2[i]!=0) { // added if statement
ierror+=(I1[i]-I2[i])*(I1[i]-I2[i]);
}
this doesn't seem to work. Please advise.

21 Aug 2012 henry wang

I have 2 images, IM1, IM2. IM2 is a filled with value of 70s over a ROI and 0s elsewhere. I want to register IM1 with IM2 such that the MSE is minimized over the region where IM2 has value of 70s. Using rigid transformation.

Is this possible to do? This is not a direct image registration problem because IM1 and IM2 are not really same image. I want to find transformation such that sum(IM2(T*x)-IM1(x))^2 is minimized where IM2(T*x)=70. I tried to modify squared_difference_double.c:
if (I2[i]!=0) { // added if statement
ierror+=(I1[i]-I2[i])*(I1[i]-I2[i]);
}

this doesn't seem to work. Please advise.

21 Aug 2012 henry wang

Great work!

Question: is there any way to display how much an image was say rotated or shifted for a rigid transformation? Say I rotate an image by 15 degrees, imregister will output Ireg but how do I output this 15 degrees? Bx,By,Fx,Fy seems not to give this information. Thanks so much.

21 Aug 2012 Ryan Wu

I found a possible bug in register_images.m
In following line which makes the transformation matrix of Affine:
M=make_transformation_matrix(x(1:2),x(3),x(4:5));
The shearing operation was not passed to the function. The correct one should be:
M=make_transformation_matrix(x(1:2),x(3),x(4:5),x(6:7));

03 Aug 2012 Ryan Wu

The error "Undefined function or method 'movepixels' for input arguments of type 'double'." was originated from the path settings.
I added the following three lines to after 'compile_c_files' in basic_demon_example.m and the problem is solved.
addpath([pwd '\functions']);
addpath([pwd '\functions_affine']);
addpath([pwd '\functions_nonrigid']);

02 Aug 2012 Michele Noccioli de Souza  
25 Jun 2012 wenfei

Hello!Problem:when mexxing,there is an error:
C:\PROGRA~1\MATLAB\R2009B\BIN\MEX.PL: Error: Link of 'movepixels_2d_double.mexw32' failed.

??? Error using ==> mex at 221
Unable to complete successfully.

Error in ==> compile_c_files at 8
mex(filename,'image_interpolation.c');

I need your help!Thanks very much!

14 Jun 2012 David Foster

Great routines, but to avoid instability with some images, is it possible to extend Options.Registration to include (1) only Translation and (2) only Translation and Resize (in x and y directions)?

26 Apr 2012 Shan Chen

Problem: when running the basic_demon_example, there is an error:
??? Index exceeds matrix dimensions.

Error in ==> movepixels at 27
I3=movepixels_2d_double(double(I1),double(T(:,:,1)),double(T(:,:,2)),double(mode));

Error in ==> basic_demon_example at 51
M=movepixels(I1,Tx,Ty);

Solution:
the 51th line in basic_demon_example.m:
M=movepixels(I1,Tx,Ty);
should be changed as follows:
T(:,:,1)=Tx;
T(:,:,2)=Ty;
M=movepixels(I1,T);
since the imput parameters didn't match properly.

20 Apr 2012 Ana

fan,

How do you managed the 'out of memory' problem? I tried to run the program in a 64byte OS, memory 3G , the size of Moving image and Static Image are both 512*512*56 and the Matlab is 64bits.

Thank you in advance.

29 Mar 2012 Sylvain

Thanks for your really good job!

I completed the test at line 161 of register_image.m, because I had 2 images 102x254 and 101x255 that need the resize step :
if(sum(abs(size(Istatic)-size(Imoving)))~=0)
instead of
if(sum(size(Istatic)-size(Imoving))~=0)

24 Jan 2012 Heng

Hi. I'm using your program to register MRI T1 and T2 images. I used [Ireg,Bx,By] = register_images(Imoving,Istatic);
it ran well at first, then it gave me "Undefined function or variable "resizepercentage".

Error in register_images (line 323)
if(resizepercentage~=1)"
this error.

Could you tell me what is wrong?
Thanks.

29 Nov 2011 yang liu

Sorry,it's my fault. With the step of "Set Path", the program run normally.
Thank you for excellent job.

29 Nov 2011 yang liu

??? Undefined function or method 'movepixels' for input arguments of type 'double'.

Error in ==> basic_demon_example at 50
M=movepixels(I1,Tx,Ty);

Error in ==> run at 57
evalin('caller', [s ';']);

After compling, above error was presented. Did I make some mistake?

28 Nov 2011 Luca  
08 Dec 2010 fan

Thank you!
so it must use a 1920M continuous memory space to create a huge array, I think ihis is the reason of "out of memory".
I tested you 3D Affine registration, but the registered Image(Ireg) is just identical to the Imoving image, and the deformation field Fx,Fy,Fz is all zeros. is there any mistake in your program?

08 Dec 2010 Dirk-Jan Kroon

*fan,
When you optimize with the quasi newton method, you need memory space for 10 x the amount of unknowns.
In your case 256 * 256 * 128 * 3 (x y z) *10 = 251 658 240 values in the Estimated Hessian, and to store the transformation fields of x,y,z and both images 256 * 256 * 128 * 5 = 41 943 040 values.
In total you store 293 601 280 values, if all those values are in double we have to store 8x this amount in bytes, is 2.2GB ...
Thus be sure to also use Matlab 64bit ..

07 Dec 2010 fan

I tried to do 3D nonrigid registration use this program, but I found that it use very large of memory. I tried to run the program in a 64byte OS, memory is 3G , the size of Moving image and Static Image are both 256*256*128. but it run to "out of memory". I found that there a very large of memory not released, I don't know how much memory it should use,so you should do much more in memory management.

07 Dec 2010 fan

so, I think that it can be use less memory if you break the large arry into many little arrays.

08 Nov 2010 arghavan

Hi Dirk
i have 3d( face ) laser scan database .
by registration i want to establish correspondenc for all points of the face, in order to after
bringing them into correspondence linear combinations of scans,are again faces. Could you please make good examples for 3D nonrigid registration which demonstrate how to set parameters for registration? thanks, arghavan.

29 Jul 2010 Cheng Lu

What a perfect work~~~ I try it and foud that the gradient of the image is calculated as [My,Mx]=gradient(M); But why you want to inverse the x and y? Since normally we use [Mx,My]=gradient(M); Maybe it is related to your 'Movepixels' function?

Your implemntation is based on the additive Demons, do you have any idea to add a compositive Demons? How do we calculate the composition of fields in Matlab? Thanks.

09 Jul 2010 sajan

hi Dirk,
Ive been using demon's off late. Had a question on the forward and backward transformation functions and its use in conjuction with movepixels.m . Here is what I have: A deformation map (D) derived by registering a moving object (M) to a static object (S). I would now like to use D^-1 and M and solve for S.

Ive tried using movepixels.m and the bacward2forward.m, but as I see it, movepixels.m only considers static images as its inputs, which is not what I desire. Your comments and suggestions on this would be highly appreciated.

Thanks

07 Jul 2010 Dirk-Jan Kroon

*emilie

The functionmovepixels.m is present in the sub-folder functions_nonrigid. To make 3D work, you have to run compile_c_files ..., or compile the c-code with the mex function.

07 Jul 2010 emilie

The file ''movepixels.m'' does not exist in the zipped folder that I downloaded. So, I searched it in the net but the version that I found does not fit to the existing 3D image registration :(
Can you please tell me where I can find the 3D version of the file ''movepixels.m''.
Thanks.

31 May 2010 yang xiaomei

good job.thanks.
I want to try the example in the demons energy,but there is an erro message for the fminsd,I can not find the information of fminsd. look forward to receiving your reply.thanks
xiaomei

15 Feb 2010 Dirk-Jan Kroon

*Vijay
Denoising the data before registration is not really needed, but when done with an edge preserving filter, it will slightly improve the final results.

13 Feb 2010 Vijay

This is an excellent algorithm... I have a quick question. Is this algorithm affected by noise in the image? Will it make sense to denoise image before doing image registration?

Thanks,
VIjay

10 Feb 2010 Toni

Just a quick question please!

So the pixel value from the moving image is transformed into the deformed moving one and the new position is e.g. x + Tx(x) , y + Ty(y), right? Does this mean that the old image is just updated with these values? what happens to the old pixel values where the pixel was transformed from and is the 'transformed to' pixel value the new value + the old one which was there already? And where does the interpolation take place?

Too much confusion....

29 Jan 2010 LI guang

sorry i made a mistake .The result in multi-registration is also good

26 Jan 2010 LI guang

I ran the example of multi-registration.but the result is not correct.The pixels of floating image turned to be choas when I ran that multi-registration.So is there something wrong about the multi-registration codes?

18 Jan 2010 Yin Yang

Hello, I know it may be a stupid, but I would like to find a function which could compute a pixel say, (x1, y1) in the moving image 's location in the static image, say (x2, y2). It seems to me that the (x1, y1) and (x2, y2) are related through the so-called transformation . Could you explain the detailed relationship among them and what exactly the direction of x, y and z in your code? (from left to right, up to down and top tp buttom?) Thanks

11 Jan 2010 Rob Campbell

oops, two ratings. But I do like the program!

11 Jan 2010 Rob Campbell  
11 Jan 2010 Rob Campbell  
05 Dec 2009 Dirk-Jan Kroon

*gx,

The equation "bins=round(numel(V)^(1/ndims(V)));" is not from literature. You can also use a fix bin size of 255, or so.

- Mutual information only works if there are overlaps in the histogram bins.
- More histogram bins will give better registration accuracy.
Thus this equation gives a good trade-off based on the number of available pixels ...

04 Dec 2009 gx

I meant how the equation "bins=round(numel(V)^(1/ndims(V)));" is obtained? Is it based on some existing publication?

04 Dec 2009 gx

Good work. Thank you.

One question: When you determine the bin size in function "registration_error_mutual_info", you use:

bins=round(numel(V)^(1/ndims(V)));

May I know what this formulation is obtained?

20 Aug 2009 Adeola

Hi Sir, your work is very good & relevant. Im still a beginner in Matlab environment. Im working on a project that is related to your work. I tried running the codes but for the basic_demon_example, it gave me an error message at line 50, that is, [M=movepixels(I1,Tx,Ty);]. Can you pls help me? Hoping to hear from you soonest.

17 Aug 2009 jichao zhao

Hi, Sir, your codes are definitely good. When I use your 3D example in register_volumes, the results shown by showcs3
looks weird. Also the values range from -0.2 to 0.3 for example.
Can you explain why it. On the other hand, when I used Ireg2=movepixels(Istatic,Fx,Fy,Fz); showcs3(Ireg2);
Ireg2, however, turns out to be surprising good. thanks.

12 Aug 2009 jichao zhao

Could you please make good examples for 3D rigid and nonrigid registration which demonstrate how to set parameters for registration? thanks, jichao

23 Jul 2009 Geoff  
07 Jul 2009 Cheng Lu

good job!

02 Jul 2009 Alper Yaman

Can you add single thread codes of the latest version. I am using linux and it gives error.
In addition, as using in linux, compilation of mex files gives error just because of the comment lines. You can avoid such errors by replacing "//" with "/*" and of course add "*/" at the end of the line.

18 Feb 2009 nor ki

works pretty fine!

13 Nov 2008 Dirk-Jan Kroon

*yichen fan
I have never seen this error.
Please have a look at the help of Mex : http://www.mathworks.com/access/helpdesk/help/techdoc/index.html?/access/helpdesk/help/techdoc/ref/mex.htm

Maybee Mex or the LCC compiler is not installed with Matlab.
You can also trie the single threaded c-code files...

13 Nov 2008 yichen fan

Having an error when compile the program:

??? Error using ==> mex
Unable to complete successfully

Error in ==> compile_c_files at 4
mex(files(i).name,'-v');

Error in ==> basic_demon_example at 7
compile_c_files

Is that a common error?
I am using Matlab ver 7.1.0.246(R14) SP3

07 Nov 2008 Dirk-Jan Kroon

*Michel Kocher...
After this weekend i will add a (previous) single threaded version, which works with the Mac computer.

07 Nov 2008 Michel Kocher

Hello, I am using Matlab from a Mac and the files system.h and process.h do not seem to be available. How can I compile movepixels_2d_double.c

31 Oct 2008 Dirk-Jan Kroon

Please upgrade to version 10b if you experience Matlab crashes with affine transformation in version 10.

28 Oct 2008 Assaf cohen

Will this be good to register a degraded image due to Atmospheric Turbulence to a reference frame (avarage of say 10 degraded images) and this how to improve the quality of the video?

22 Oct 2008 Dirk-Jan Kroon

*K K,
Thanks for your comments. The method uses backward warping. Today, I will look at my code if I accidentally swapped Tx and Ty. This week or the next I will upload a new version, which can be used with any Matlab optimizer.

* Franz Rudolf
This transformation algorithm is called: non-parametric, iconic feature based, using point features.

21 Oct 2008 K K

It seems that the Tx and Ty are indeed swapped???
I have tried the code on a very simple line registration, the "registered image" is correct, however, Tx and Ty seem being swapped...

21 Oct 2008 K K

I test the code by adding the following:

% Register image 1 to image 2
[I3,Tx,Ty]=demonregistration(I1,I2,[],true);

[h,w] = size(Tx) ;
Ty = zeros(h,w) ;
Tx = 5*ones(h,w) ;

I3=movepixels(I1,Tx,Ty);

but the result is not what I expected.
The image is shifted up instead of left~~~
Indeed what is Tx,Ty doing? is it a deformation field? forward or backward warping?

21 Oct 2008 Franz Rudolf

I am a student and want to learn something about nonrigid registration techniques. Can anybody tell me which transformation model it uses (is the Thin Plate Transformation the same as the B Spline?)

13 Oct 2008 K K

thanks a lot. I know what you mean. But what I mean is change the Idiff as something like this:
Idiff_color=M_color-S_color;
Idiff = Idiff_color(:,1)+Idiff_color(:,2)+Idiff_color(:,3) ; Idiff = Idiff/3 ;
where M_color is color version of M previous obtained.

13 Oct 2008 Dirk-Jan Kroon

* K K,
Color image registration example:
C1=im2double(imread('lena1.jpg'));
C2=im2double(imread('lena2.jpg'));
[I3,Tx,Ty]=demonregistration(rgb2gray(C1),rgb2gray(C2),[],false);
C3 = zeros(size(C1));
C3(:,:,1)=movepixels(C1(:,:,1),Tx,Ty);
C3(:,:,2)=movepixels(C1(:,:,2),Tx,Ty);
C3(:,:,3)=movepixels(C1(:,:,3),Tx,Ty);
imshow(C3,[]); title('Registered image');

13 Oct 2008 K K

I try to complie it with other machine, thanks. Would like to know if you have version for color image~ Thanks~

13 Oct 2008 K K

Hi, seems it is good. But I cannot complie it..is it due to the Matlab version? I have R2006a and Matlab 6.5. both cannot complie. Thanks a lot!

17 Sep 2008 Dirk-Jan Kroon

There is a small bug that images with odd valued dimensions now gives an error. Will be updated tomorrow...

Updates
24 Oct 2008

Algorithm rewritten to be used with Matlab Optimizers

10 Nov 2008

Add single threaded MEX code

25 Mar 2009

Out of the box registration now available and also multiple modalities support through modality transformation

14 Jul 2009

Now Linux multi-threading compatible, added cubic interpolation.

16 Jul 2009

3D cubic interpolation bug fixed...

14 Aug 2009

Fixed major bug in 3D registration by adding lost "uz direction" to error term reported by Vivek. Fixed single cubic interpolation bug.

08 Sep 2009

Fix Gaussian Filter

01 Oct 2009

Linux Ubuntu Tested

03 Jun 2010

Fixed example of sub-function, updated affine mutual information function.

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