Comments and Ratings

*Christos

Thank you for your bug report, I will try to fix them in the next code update.

Best regards, Dirk-Jan

you need to put t=0 if the expression in the if does not stand

if( isempty(Mask) | (~isempty(Mask) & ~isempty(find(Mask~=0) ) ) )
 
   %your code
   if(size(U,3)==3),
   .....
   end
else
    t = 0;
end

This seriously looks like great stuff, unfortunately, I can't get the c file to compile..

icc: command line warning #10157: ignoring option '-w'; argument is of wrong type
icc: error #10104: unable to open 'all'
mex: compile of ' "eig3volume.c"' failed.

Any help?? Thx in advance!

Dear Hui,

(1) Indeed 'p' doesn't exist, I will replace it with 'd' in the next update.

(2)
The scaling [1 1 1 0.1 0.1] is because the parameters are [translateX translateY rotate resizeX resizeY]. If you change the size of the image only a little bit it will produce large pixel movements. An optimizer produces the best result if all parameters have approximately the same influence on the image transformation, thus we introduced the scaling.

Dirk-Jan Kroon

Hi, Dirk,

Thanks for sharing the excellent codes.
I have two questions about your version18e codes:

1. In image_difference.m, line 34, if(exist('type','var')==0), type='p'; end. should here type = 'd' as default? Because there is no type 'p'

2. In example_2d_affine.m, can you explain a little bit about why the scale = [1 1 1 0.1 0.1] needed here? I didn't figure out the purpose of scale here.

Thanks very much.

Hui

*ciaiaia ccccccc
The error is very clear it cannot find the file, probably you executed the MEX command from a different folder ?

Otherwise try "mex -setup" to reset your compiler settings.

Does this work with R2007a? Thank you

The function 'normxcorr2' available in matlab is faster than the code you submitted. Please profile it and see for yourself. But thanks for sharing the code.

I uploaded a new version with derivative boundary check bug fixed, probably tomorrow online. thnx Elmar.

I permuted the directions of the volume so that it is 147x227x227, now it works perfectly

Thanks for sharing this tool! works very well and fast, but i'm experiencing some problems:
I'm trying to filter a 3D MRI volume of size 227x227x147. Depending on the value of 'rho' I use I get a variable number of slices in the third dimension that are all 'NaN'. The bigger rho, the more NaN slices are in the output image volume. For every value of T used the number of NaN-slices accumulates, so that after several timesteps the whole image volume consists of NaNs.
What could be the reason for the NaNs in the output?

My original image is single and normalized to a range of 0 to 1 and does not contain any NaNs.
thx, Elmar

Outstanding! Sometimes has an error when I switch to a different rendering mode. Thanks for this application.

That is great, many thanks for sharing, all the forks. I am wondering whether somebody here uses a similar idea to obtain fiber orientations from 2D/3D images. I guess it uses the eigenvectors and eigenvalues of gradient matrix of the input images.

can this capability be compiled into a standalone application using the matlab compiler?

Could list a few references that we can read on this filter, implementation any literature for the implementation please? Thank you

awesome!

Perfect. It is fast and robust.
Thank you

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.

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.

Thank both of you, Brian and Dirk-Jan Kroon, cheers, jichao zhao

*jichao zhao
showcs3 always uses the default Matlab image ranges, thus if a double or single it sets black to 0 and white to 1, and if uint8 black to 0 and white to 255.
That your image range is 0 to 60 instead of 0 to 1 will influence registration, because the pixel based penalty will now be larger in comparison to the smoothness penalty.
I almost always normalize my data to range [0..1] by V=V-min(V(:)); V=V./max(V(:));

When I used the function "showcs3", my input images are pure black
and white, but when I used matlab built-in fucntion imagesc, I can see my images are gray color instead of pure black and white. Also when I use colormap, I can see the color ranges from 0 to 60. So my question is that why my images are pure black-white when plotted using showcs3 and whether it influences results of registration or not. Many thanks. If you need, I can send you my image data. thanks, jichao