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Hessian based Frangi Vesselness filter

version 1.11 (3.88 MB) by

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

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50 Ratings

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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

Comments and Ratings (86)

Haoyi Liang

When I run Ivessel=FrangiFilter2DInternet(I);
I get the error "Assignment has more non-singleton rhs dimensions than
non-singleton
subscripts

Error in FrangiFilter2D (line 96)
    ALLfiltered(:,:,i) = Ifiltered;"

Can anybody help

Rohan Singh

hello, any one please help me out that how to execute the all files in matlab sorry for this lame question but i am new in matlab development please help me urgent, thankyou in advance

Filip Vesovic

Alex

Alex (view profile)

Out of memory when I run it code. How to deal with this problem?

Samuel Geurts

@reza and Somayeh Ebrahimkhani, maybe you have to compile eig3volume.c first.

Hi ,
I tried to download the file, but eig3volume.m function is empty. Can someone please share the code of this function with me?
Thanks

reza

reza (view profile)

hi,

why is eig3volume.m function empty? 2D version works fine but for 3D version , the mentioned function is needed! could you please add the function?

Weblink Wang

Hello. I try to run the code, but I haven't got any result. Is there any step to follow to run this code?
Thank you!

Never mind my previous comment. For those ones having problem to compile the mex file, I found the compiled version here [1] and they worked very good. Dear Dirk-Jan, you must to comment the line 129 on FrangiFilter3D.m.

[1] https://github.com/shayo/Planner/tree/master/MEX/Win_x64

Thank you for the code. Is that possible to you give me the compiled (C++) files? I'm having some wierd problem on my matlab that is not detecting the compiler...

Faiza Bukenya

Thank you so much for the code. the code works, however I have a problem with displaying the result.Error using isosurface (line 75) V must be a 3D array.

mohammed

Can this method can be used for 3D blood vessel tracing of OCT-B scans?

Works great thanks so much

I'm working in a project about arteries segmentation, and I need this module. As you said, eig3volume.c is empty. How can I use it in windows?

Ilya Belevich

Nicole Cliner

Hi friends
I'm working on a project about counting active sperms in images, I have found the active cores and my problem is that I can't detect tails in image,I don't know how o detect only tails in image,and how to recognize which core is for detected tail.please help me solve this problem! as soon as possible

the function eig3volume.m is empty,how should i do?

Asmat khan

Dear Sir,
Please send me the work that you implemented.
As you mentioned
see pp. 45

Portgas Ace

>> mex eig3volume.c
 
  C:\PROGRA~1\MATLAB\R2013A\BIN\MEX.PL: Error: 'eig3volume.c' not found.
 
Error using mex (line 206)
Unable to complete successfully.
 

How do i fix this?

Portgas Ace

how do you run this code?

elnaz ezzati

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?

fa.abdoly

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

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

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??

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??

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

Gary Tsui

Ian

Ian (view profile)

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

Sarun

Sarun (view profile)

Works great!!

yezi

yezi (view profile)

yezi

yezi (view profile)

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?

alaa

alaa (view profile)

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.

Lupine

Lupine (view profile)

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 ?

any

any (view profile)

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

feng

feng (view profile)

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

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.

galaxy

galaxy (view profile)

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?

G.Liz

G.Liz (view profile)

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

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.

mona

mona (view profile)

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?

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?

Joy King

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

Marija

Marija (view profile)

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.

Lee

Lee (view profile)

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.

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!

ikaraq

ikaraq (view profile)

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

Yonas Haile

thanks a lot, its very useful

jue jiang

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

bahar cham

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++

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...

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)

Dirk-Jan Kroon

Dirk-Jan Kroon (view profile)

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

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!

Weiguang Ding

very helpful! thanks!

Rui

Rui (view profile)

super useful. thank you very much!!!

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.

Omar

Omar (view profile)

Very useful and instructive

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?

Sven

Sven (view profile)

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

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!

Amanda

Amanda (view profile)

Thank u. It realy helps me a lot!

Alan

Alan (view profile)

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?

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.

ted p teng

ted p teng (view profile)

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/

ted p teng

ted p teng (view profile)

J Abraham

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

jichao zhao

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

Bruno Afonso

This was a very handy implementation! Thanks.

Brian

Brian (view profile)

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

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.

Dirk-Jan Kroon

Dirk-Jan Kroon (view profile)

*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.

Dirk-Jan Kroon

Dirk-Jan Kroon (view profile)

*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.

Walter

Walter (view profile)

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.

Mehmet OZTURK

Sven

Sven (view profile)

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

Updates

1.11

Update help Frangi 3D (Description of parameters)

1.10

Changed comment, enabled the sigma scale correction

1.9

2D eigenvector fix

1.8

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

1.6

Fix Gaussian filter function

1.5

Bug fixed in direction of edge returned by eig3volume.c

1.4

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

1.3

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

1.1

Scaling normalization sigma to sigma^2

MATLAB Release
MATLAB 7.8 (R2009a)
Acknowledgements

Inspired: Microscopy Image Browser (MIB), GraphTrace

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