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Hessian based Frangi Vesselness filter

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Hessian based Frangi Vesselness filter

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11 Jun 2009 (Updated )

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

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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)
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Comments and Ratings (58)
26 Jun 2014 elnaz ezzati  
24 Jun 2014 Christian

Thank you very much for this useful program. One question: I think in FrangiFilter3D.m line "(2*options.FrangiC^2)" on line 128 could be replaced by "C" because of line 120, couldn't it?

22 Jun 2014 fa.abdoly

Hello,I want to seprate vessel and airway by this submission but i can't.can anybody help me?

21 Jun 2014 Preetham Aghalaya Manjunatha

Very well written code. Useful to extract many curvature dominant features in image.

11 Jun 2014 Sara Saeed

Can anyone help me what was meant by c (max.of hessian norm) ? Is it the max of the norms all over the image in a certain scale ,or it's the maximum norm across all scales??

11 Jun 2014 Sara Saeed

Can anyone help me what was meant by c (max.of hessian norm) ? Is it the max of the norms all over the image in a certain scale ,or it's the maximum norm across all scales??

15 Apr 2014 VISWANATH YESHWANTH  
09 Apr 2014 Christian Baumgartner

Hi Dirk,

the submission seems to work very well. Thanks for your effort! Just a detail, did you forget a 'keyboard' statement when debugging 'FrangiFilter3D' on line 129? Or is this intentional?

Cheers, Chris

25 Dec 2013 Gary Tsui  
09 Dec 2013 Ian

Hi, sir,

Mostly it works. But I found some minor problems (Might be my problems):
1. The 2D version, the Direction is not correct. I used cos and sin function and then the "quiver" function to draw them, it seems the Direction matrix doesn't reflect the main direction of the vessel structure.
2. For 3D version, it would be great if you can provide me not only the main direction but also the 2 sub-directions related with the 2 "larger" eigenvalues.

Thanks for your work. Please tell me what's wrong with the 2D direction.

Ian

26 Nov 2013 sarun

Works great!!

25 Sep 2013 xia  
25 Sep 2013 xia

thank u very much for the Frangi2D code!I've tried it on my digital substraction aniography image sequence(brain vessel).The code worked well on most vessels. But my main vessel owned a dark background because of the complex tissue, so the results were not so good, maybe the parameters need adjusting. Would you please give some advice on how to preprocess the dark background of the complex vessel part?

09 Sep 2013 alaa

hello, i am working on a 2D cardiac images and i used frangie filter to highlight the vessels, but i have problems in images containing narrow vessel, and i am not sure that i effectively enhance the contrast of the images before using frangie filter,can i have any help about improving the contrast of images,i have to mention that i tried the contrast stretching, histogram equalization, adaptive histogram equalization.

23 Jul 2013 Lupine

Hello,I have tested them,but I use the Hessian2D only,I dont't know how to use the eigenvalues and eigenvectors .Who can help me ?

06 Jul 2013 any

Hi,i use a frangi filter for a vessel extraction,it's ok...after i have a problem to obtain a binary image...i don't know how do...you have a idea?i use otsu threshold but the result is not good...Can you help me??? thank you

02 Jul 2013 feng

who can tell me why there's nothing in the file "eig3volume.m"

03 Jun 2013 Lauren Haaitsma

Hello galaxy,

To use eig for 3D images you don't need a 3D matrix, you only need a 3x3 matrix.
For blob detection you need to use eig on the Hessian matrix of the 3D data. So for example:
>> hessian = [
Ixx,Ixy,Ixz;
Ixy,Iyy,Iyz;
Ixz,Iyz,Izz
];
% where Ixx is the second order gaussian derivative of the image in the x direction and Ixy is the partial derivative in the x and the y direction, you'll have to calculate these items using Hessian3D or a similar function.
[V,D] = eig(hessian); %V is a 3x3 matrix of eigenvectors in the columns and D is a 3x3 matrix with eigenvalues in the diagonal.

Hope this helps.

02 Jun 2013 galaxy

Dear Lauren Haaitsma,
I want to detect tubular and blob structures, but I've problem with eig3volume as you said.I think it can not detect in 3D properly..How did you use "eig" in matlab for 3D images?

31 May 2013 G.Liz

sir, could you please tell me the order in which i should run these files for a 2D image.

28 May 2013 Lauren Haaitsma

I've only used the 3D filter so far, but I've found that the eigenvalues calculated by the eig3volume are different from the ones from Matlab's 'eig' function. Furthermore the distinction between tubular structure and blob is more pronounced using Matlab's 'eig'. It is a bit slower however.
There is also a stray 'keyboard' in the FrangiFilter3D, which I think should have been removed.
Other than that it's a great and very useful submission.

04 Mar 2013 mona

This is really good for radiology but when I am trying to run the exmaple pf FrangiFilter2D over other coronary angiogram images, its giving me the following error: Assignment has more non-singleton rhs dimensions than non-singleton subscripts. Any suggestion?

05 Feb 2013 mina kh

thank you for your good code
2D code gives good results for CT lung images (enhance vessels very well) but in 3D, instead of enhanced vessels some circles appear and result isn't good.please help me why?

12 Oct 2012 Joy King

what should I do when the K>> comes up running the 3D version.

11 Jul 2012 Marija

Lee, the code is okay, when Lambda1 and Lambda2 are passed from eig2image their values are actually switched (check line 108 in FrangiFilter2D).
My question would be, has anyone tried testing the 3D algorithm on a series of MRI scans?
I take 56 scans, load them into one array but can't seem to get the vessels out. Could this be because the resolution between slices is greater then intra-slice resolution?
Any idea is greatly appreciated.

08 Jul 2012 Lee

Very nice code - saved me a lot of time. I may be mistaken, but I think there is a problem in FrangiFilter2D, where you define Rb = (Lambda2./Lambda1).^2 on line 83. This contradicts the original paper, assuming Lambda1 > Lambda2. Rb is defined as deviation from blob-ness and should achieve a maximum value of 1 if Lambda1 == Lambda2.

16 Apr 2012 Ricardo Corredor

I already did different tests and I found it very useful and easy understandable. However, one question recently arrived according to sigma values: are these terms measured in milimeters or in voxel units? (it is maybe a matlab question about convolution) . And this sigma corresponds to the tubular object radius or diameter? Thanks!

19 Jan 2012 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

06 Dec 2011 Yonas Haile

thanks a lot, its very useful

01 Dec 2011 jue jiang

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

23 Nov 2011 bahar cham  
19 Nov 2011 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++

20 Sep 2011 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...

20 Sep 2011 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)

29 Aug 2011 Dirk-Jan Kroon

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

23 May 2011 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!

18 Apr 2011 Weiguang Ding

very helpful! thanks!

08 Apr 2011 Rui

super useful. thank you very much!!!

10 Jun 2010 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.

20 Apr 2010 Omar

Very useful and instructive

04 Apr 2010 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?

17 Mar 2010 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

17 Nov 2009 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!

06 Nov 2009 li

Thank u. It realy helps me a lot!

24 Sep 2009 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?

20 Sep 2009 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.

20 Sep 2009 ted p 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/

20 Sep 2009 ted p teng  
14 Sep 2009 J Abraham

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

12 Aug 2009 jichao zhao

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

11 Aug 2009 Bruno Afonso

This was a very handy implementation! Thanks.

24 Jul 2009 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

15 Jul 2009 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.

10 Jul 2009 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.

10 Jul 2009 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.

08 Jul 2009 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.

15 Jun 2009 Mehmet OZTURK  
13 Jun 2009 Sven

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

Updates
10 Jul 2009

Scaling normalization sigma to sigma^2

10 Jul 2009

Sorted the eigenvalues by abs(eigenvalue), this does not influence the output result in case of vessel images. Also new input option added.

17 Aug 2009

C-code comments from // to /* */ for better linux compiler support.

26 Aug 2009

Bug fixed in direction of edge returned by eig3volume.c

08 Sep 2009

Fix Gaussian filter function

02 Oct 2009

Fixed bug in 3D in Dxy -> Dxz , which caused the sigma scaling not to work.

27 Oct 2009

2D eigenvector fix

01 Dec 2009

Changed comment, enabled the sigma scale correction

02 Mar 2010

Update help Frangi 3D (Description of parameters)

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