version 1.11.0.0 (3.88 MB) by
Dirk-Jan Kroon

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

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

Dirk-Jan Kroon (2021). Hessian based Frangi Vesselness filter (https://www.mathworks.com/matlabcentral/fileexchange/24409-hessian-based-frangi-vesselness-filter), MATLAB Central File Exchange. Retrieved .

Created with
R2009a

Compatible with any release

**Inspired:**
Microscopy Image Browser (MIB), Microscopy Image Browser 2 (MIB2), Jerman Enhancement Filter, GraphTrace

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Dennis zTaisuke MorinoGregory PostolskyDoaa MohamedChris HwangI am having trouble applying this filter on my angiogram. I am able to run the filter on the example image (vessel.png), but when I try to run it on my own image, i get the following error message:

"Assignment has more non-singleton rhs dimensions than non-singleton subscripts

Error in FrangiFilter2D (line 96)

ALLfiltered(:,:,i) = Ifiltered;"

Would really appreciate some insight. Thanks!

mcdull hallAs Cris Luengo, to use imgaussian in MATLAB2017a after in 64bit machines, either mex with -compatibleArrayDims, or change the type of ndimsI and dimsI[] from int to mwSize in mexFunction.

Cris LuengoTo those having a problem with `imgaussian`: You need to compile the MEX-file with the `-compatibleArrayDims` option, as it uses `int` instead of `mwSize` for array sizes.

BERKAY YUCELPawan SupulWorks perfect for me. Thank you

PhillipI have been playing around with this and just wanted to say, that it works very well, other than for the hideous edge effects which can be neatly dealt with by adding the 'replicate' argument to the imfilter call in Hessian2D.m, i.e.

Dxx = imfilter(I,DGaussxx,'conv','replicate');

Dxy = imfilter(I,DGaussxy,'conv','replicate');

Dyy = imfilter(I,DGaussyy,'conv','replicate');

LailaExcellent.

Laveena KewlaniAvery BermanRegarding the memory request error in imgaussian described below by Gregory, this appears to be a function definition issue with newer versions of MATLAB/mex in the function mxCreateNumericArray. A quick fix is to change the function imgaussian.c:

Change both lines of the form

plhs[0] = mxCreateNumericArray(ndimsI, dimsI, ...

to

plhs[0] = mxCreateNumericArray(ndimsI, dimsI_const, ...

Then recompile by running "mex imgaussian.c".

Avery BermanI'm not sure what happened to my previous, here it is again:

Regarding the memory request error in imgaussian described below by Gregory, this appears to be a function definition issue with newer versions of MATLAB/mex in the function mxCreateNumericArray. A quick fix is to change the function imgaussian.c:

Change both lines of the form

plhs[0] = mxCreateNumericArray(ndimsI, dimsI, ...

to

plhs[0] = mxCreateNumericArray(ndimsI, dimsI_const, ...

Then recompile by running "mex imgaussian.c".

Siming sophie BayerHi Gregory,

I have run into the same problem. Did you solved this problem?

GregoryI think there is a problem with the imgaussian function. I am trying to run on a 10x512x512 CT image and get this error:

Error using imgaussian

Requested 42949672970x140037408686090x140039176060928 (17179869184.0GB) array exceeds maximum array

size preference. Creation of arrays greater than this limit may take a long time and cause MATLAB to

become unresponsive. See array size limit or preference panel for more information.

I have tried casting the data to different types (single, double, int16, int32, etc.) and taking a subsample of the image (10x10x10), but I still get this error with the some outrageous amount of memory requested.

Anyone have thoughts on why this is happening?

Urs HofmannI think there is a bug in the 2d analysis. As far as I know, the scale is defined as scale = sigma^2. In the code its set to scale = sigma.

ANITA KHANNAplease guide me how to use this for airway detection of 2D CT lung vessel

Mounika RapoluMounika RapoluHi everyone,

Thanks for the discusion.

This Frangi-filter enhances individual line-like structures, not their intersections. To enhance or detect junctions what should be done??

wenhao xutronBeena61This does not implement the algorithm described in Frangi's paper - there are several conceptual issues with the code, such that this "kind of" detects vessels, but not with the same results as one would with the correct algorithm.

LenaThe Matlab code run successfully. But a problem that "Undefined function or variable "Dxy". The first assignment to a local variable determines its class" occured when I try transfer the code to c++ by "mex". Is there any help? Thanks a lot.

charlesThis is exactly the filter that I need. I only have one problem with running the script, I do not know how to compile the eig3volume.c. Have tried googling it and tried using the mex function but it all didn't work out for me. Can anyone help me with this please. Give me some intructions on how to do it or simply send the matlab script which is already compiled (if it works that way)

Best of regards,

Charles

adrien mangeI precise that I want to use the FrangiFilter2D function

adrien mangeHi, what is the syntax to call the function changing some options values ?

amr elsawyThanks

For the error, make sure that the image is grayscale

zohreh hosseinaeeJohan Djurhuus MyreHaoyi LiangBelén MartínWhen 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 SinghAsadullah Mumtazhello, 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 VesovicqwdasdAsd aDDADAqwdasdAsd aDDADAAlexOut 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.

Somayeh EbrahimkhaniHi ,

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

Thanks

rezahi,

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 WangWeblink Wang*Maëlle BLANCO de la TORRE

see

https://www.mathworks.com/matlabcentral/answers/84794-edge-detection-using-the-hessian-based-frangi-vesselness-filter

Maëlle BLANCO de la TORREHello. 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!

Helder OliveiraNever 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

Helder OliveiraThank 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 BukenyaThank 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.

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

Jérôme ProulxWorks great thanks so much

Alejandro CasoI'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 BelevichNicole ClinerHi 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

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

razieh azizianAsmat khanDear 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 Acehow do you run this code?

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

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

Sara SaeedCan 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 SaeedCan 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??

VISWANATH YESHWANTHChristian BaumgartnerHi 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 TsuiIanHi, 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

SarunWorks great!!

yeziyezithank 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?

alaahello, 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.

LupineHello，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 ?

anyHi,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

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

Lauren HaaitsmaHello 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.

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

Lauren HaaitsmaI'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.

monaThis 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 khthank 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 Kingwhat should I do when the K>> comes up running the 3D version.

MarijaLee, 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.

LeeVery 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.

Ricardo CorredorI 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!

ikaraqfor 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 Hailethanks a lot, its very useful

jue jiangvery useful to me

maybe i need to transfer it to c or c++

bahar chambahar champlease 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++

MaartenUpdate: 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...

MaartenThank 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*svetlana

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

svetlanaThank 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 Dingvery helpful! thanks!

Ruisuper useful. thank you very much!!!

sdf adfgIts 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.

OmarVery useful and instructive

ingenieur infosHello.

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?

SvenFor 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 ChiuThis 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!

AmandaThank u. It realy helps me a lot!

AlanThis 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 zhaoThat 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.

pangyutengi'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/

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

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

Bruno AfonsoThis was a very handy implementation! Thanks.

BrianJichao,

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 zhaoHi, 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*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*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.

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