Hessian based Frangi Vesselness filter

Enhancement of Vessel/ridge like structures in 2D/3D image using hessian eigen values

Description

This function uses the eigenvectors of the Hessian to compute the likeliness of an image region to contain vessels or other image ridges , according to the method described by Frangi (2001)

It supports both 2D images and 3D volumes.

The 3D method contains an c-code file which can calculate fast the eigenvectors and eigenvalues of a list of image Hessians. First compile this code with "mex eig3volume.c"

Try the examples.
- The 2D example detects vessels in an x-ray image
- The 3D example detects an aortic stent in a CT volume

• Required Products: Image Processing Toolbox
• MATLAB release: MATLAB 7.8 (R2009a)

[Sven]

Thank you for this implementation. I had just begun to try to implement this myself, and your solution has been very helpful.

[Mehmet OZTURK]

 

[Walter]

I think there is an error. The ratio of the eigenvalues is not always correct. They must ordered by their abs value before. In your implementation this is not true.
Second point : the normalized derivatives of Lindeberg. In the normalization you should use sigma^2 and not sigma. Maybe I am wrong but it is strange that the paper of Frangi (1998) contains the same error.

[Dirk-Jan Kroon]

*Walter
The c-code already contains an section which sort the eigen values by abs value, starting with the following comment:
/* Sort the eigen values and vectors by abs eigen value */

This implementation is made from Frangi paper, thus yes if Frangi is wrong and it must be sigma^2 instead of sigma it is also wrong in this current version of the code.

[Dirk-Jan Kroon]

*Walter
I have checked the 2D eigenvalue code which was original written by M. Schrijver, and you are right the eigenvalues are not sorted in 2D by abs(value), (it is also not needed with angiogram images such as included). I will post an update today on Mathworks. Thank you again for your comment.

[jichao zhao]

Hi, Kroon. Thank you very much for your post. I found that your several posts are very helpful. When I tried to implement your codes, I came cross the following errors. Could you tell me how to fix it:

mex eig3volume.c
eig3volume.c:21: error: expected identifier or '(' before '/' token
eig3volume.c:101: error: expected identifier or '(' before '/' token
eig3volume.c: In function 'mexFunction':
eig3volume.c:258: error: expected expression before '/' token
eig3volume.c:265: error: expected expression before '/' token
eig3volume.c:280: error: 'i' undeclared (first use in this function)
eig3volume.c:280: error: (Each undeclared identifier is reported only once
eig3volume.c:280: error: for each function it appears in.)
eig3volume.c:280: error: 'npixels' undeclared (first use in this function)

    mex: compile of ' "eig3volume.c"' failed.

??? Error using ==> mex at 207
Unable to complete successfully.

[Brian]

Jichao,

I ran across your post since I was looking how to solve the same problem for another file. I found out it was because the compiler could not handle the new C99 comments of the form "//", changing them to the original C comment style of "/*" and "*/" fixed my problem. I found this info (with more details) here:
http://www.mathworks.nl/matlabcentral/newsreader/view_thread/169199

[Bruno Afonso]

This was a very handy implementation! Thanks.

[jichao zhao]

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

[J Abraham]

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

[Ted Teng]

 

[Ted Teng]

i've actually made a video on this topic if your interested.
http://www.youtube.com/watch?v=4NogJnBipu0
and here are some papers for you to read.
Frangi, A., et al., Multiscale vessel enhancement filtering,
http://www.springerlink.com/content/a57784628587870p/
Krissian, K., et al., Model-based detection of tubular structures in 3D images,
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.98.4723&rep=rep1&type=pdf
http://doi.ieeecomputersociety.org/10.1109/MMBIA.1996.534065
Aylward, S.R., et al., Initialization, noise, singularities, and scale in height ridge traversal for tubular object centerline extraction, http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=993126
Sata. Y., et al., 3D multi-scale line filter for segmentation and visualization of curvilinear structures in medical images, http://www.springerlink.com/content/d8752l41j884u249/

[jichao zhao]

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.

[Alan]

This is a great application! I was wondering if anyone could recommend a suitable value of sigma for segmenting Arteries in a brain MRI? Is the default value of sigma suitable?

[li]

Thank u. It realy helps me a lot!

[PX Chiu]

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!

[Sven]

For large volumes where memory issues may appear in the Hessian3D function, the following alteration can help in the gradient3 subfunction:
Change:
% Take centered differences on interior points
D(2:k-1,:,:) = (F(3:k,:,:)-F(1:k-2,:,:))/2;

To:
try
        D(2:k-1,:,:) = (F(3:k,:,:)-F(1:k-2,:,:))/2;
    catch ME
        warning(ME.identifier, [ME.identifier '. Attempting line-by-line filter to save memory'])
        for thisIdx = 2:k-1
            D(thisIdx,:,:) = (F(thisIdx+1,:,:)-F(thisIdx-1,:,:))/2;
        end
    end

[ingenieur infos]

Hello.
thank you for this code, but I haven't understood some things.
For example, in the Frangi2D.m, what's :
 if(options.BlackWhite)
        Ifiltered(Lambda1<0)=0;
(what is pp.45?)
and how can I calculate the direction of a vessel and according to what this direction is calculated?
Please can you explain more this code?

[Omar]

Very useful and instructive

[sdf adfg]

Its very very useful.
Can you please explain me how to interpret the 'Direction matrix' ?
What the angles assigned to every pixel mean? Does it suggest the angle of the next pixel to be included on the ridge?
Thanking you in anticipation.

[Rui]

super useful. thank you very much!!!

[Weiguang Ding]

very helpful! thanks!

[svetlana]

Thank you for the code!
Would you be able to help with an error?
I am getting the error when I try to "Attempt to execute SCRIPT eig3volume as a function".
Actually the eig3volume.m is empty...
thank you in advance!

[Dirk-Jan Kroon]

*svetlana
you have to compile eig3volume.c (see the example in the help) to use the function

[Maarten]

Thank you for the code! It works quite good in 2D for µCT data of geological samples with narrow fractures!!

However, I do not get the 3D version to work; already not with the "ExampleVolumeStent". Compiling eig3volume.c with Visual C++ Express 2010 seems to go fine, but when running the code on the example it shows "Current Frangi Filter Sigma: 1" (as it should), but then returns "K>>" and "waiting for input". What could be the reason for this?

(I'm running Matlab R2010a on a Win64 PC)

[Maarten]

Update: It DOES work when running it stepwise in the debugger. Either by running it stepwise or pressing continue. Apparently the problem comes up for every sigma, as for e.g. 3 sigma steps, I have to press continue 3x, when the K>> comes up, to get to the end result...

[bahar cham]

please help. first i run it, i faced of this error:
 Error using ==> mex at 208
Unable to complete successfully.
I don't remember exactly but it guided me to download "install Microsoft Visual C++ 2010 Express and Microsoft Windows SDK 7.1". But I have problem for install SDK. I am confused! what I should do? my OS is windows 7. You think I should change my OS? I use 7.12 R2011a. an old version will help me? I need use your perfect program. why you have written it in form of c++

[bahar cham]

 

[jue jiang]

very useful to me
maybe i need to transfer it to c or c++

[Yonas Haile]

thanks a lot, its very useful

[ikaraq]

for analysis reason, why should the process is growing inside the loop?
then... How do you generate your kernel? What mathematic basic to generate your kernel (in Hessian2D.m) ? thx