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26 Feb 2015 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin Jonas Zimmermann

Hi Christian,
Thanks for this nice implementation. However, there's a memory leak, because pbCandidate (or rather the data it points to) never gets deallocated.
How about allocating it with
pbCandidate = new bool [lNX * lNY * lNZ];
and deleting it after while block:
delete[] pbCandidate;

4
30 Nov 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Jose

Jose (view profile)

Just to follow up, that solved my problem.
Thanks!

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30 Nov 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Jose

Jose (view profile)

5
26 Nov 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Christian Wuerslin

Hola Jose,

I recently installed R2014b and had the same problem. For R2014b, the eventdata of the mouse wheel callback was changed to an object instead of a struct. The solution is to add this line

if isobject(iCnt), iCnt = iCnt.VerticalScrollCount; end

a few lines above the line which throws the error (just next to a very similar line, which checks for a struct). I will also upload a fixed version soon.

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24 Nov 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Jose

Jose (view profile)

Hi Christian,

I use imagine a lot and I think it's a great tool. However, I just upgraded to OSX Yosemite and I had to get Matlab R2014. The new imagine version works but the mouse scroll function to explore through slices seems to be broken. Here is the message I get when I try to use it:

----
Error while evaluating Figure WindowScrollWheelFcn

Undefined function 'plus' for input arguments of type 'matlab.ui.eventdata.ScrollWheelData'.

Error in imagine/fChangeImage (line 1847)
iNewImgInd = SData(iSeriesInd).iActiveImage + iCnt;
----

Any quick fix for this?

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01 Nov 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Christian Wuerslin

Thanks for letting me know, Jacob. I work on windows, soI don't get that error. Will also be fixed in a nes release sool.

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31 Oct 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Jacob Matthews

Had a followup error in which matlab couldn't find icon lw.png. It was in the icons folder but named with a capital 'L'... fixing it was the last error. Just a heads up!
Jacob

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31 Oct 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Christian Wuerslin

Hi Jacob,

I see the problem. The file is in the subfolder "Colormaps", but I only add that folder to the path a few lines later. I will upload a fixed version soon (along with some other bugfixes). Until then, you can either add the imagine subfolders to the path manually or move the block that is commented "Set some paths" up a few lines such that they are executed before the "load('mylines.mat');" command.
Sorry and thanks for letting me know.

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29 Oct 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Jacob Matthews

Hi Christian,
Loved the original release. Use it for quick visualization all the time.
Just downloaded v2, but when I try to run the imagine function it errors on line 120 trying to load mylines.mat which doesn't exist. Am I missing something obvious? Or could this be a version issue?
Thanks,
Jacob

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23 Oct 2014 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin Christian Wuerslin

Hi TAY,

nothing. In your case, just pass the gradient magnitude image to the region growing instead of the image. Something like:

[dX, dY] = gradient(image);
gradmag = sqrt(dX.^2 + dY.^2);
mask = RegionGrowing(gradmag, threshold, seed);

Cheers, Christian

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23 Oct 2014 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin TAY

TAY (view profile)

hi, may i know which part of the code shall i modify so that the seed growing is depend on the gradient magnitude of the image.

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26 Sep 2014 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin Felix

Felix (view profile)

Excellent submission!
However I added an input test to prevent my Matlab from crashing in case of homogeneous input:

if isscalar(unique(dImg(:))), error('All values inside dImg are equal!'); end

5
18 Sep 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Ibraheem Al-Dhamari

Hi,
I tried to load DICOM images but I get this error:
============================
Undefined function or variable "SNewData".
Error in imagine/fLoadFiles (line 1465)
for i = 1:length(SNewData)
Error in imagine/fMenubarClick (line 475)
SNewData = fLoadFiles(csFilenames);
Error while evaluating image ButtonDownFcn
===============================
Is it not supported?
Thanks
Ibraheem

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29 Jul 2014 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin Christian Wuerslin

Hola Joao,

you need to set up the mex compiler by typing
>> mex -setup
and then chose one of the shown options (you should at least have the lcc compiler). Then try to run the region growing again.

Christian

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21 Jul 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Patrick

5
05 Jul 2014 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin João Ribeiro

Hi Christian!
I got this error! Can you help me?! Thank you very much. :)

Trying to compile mex file...Error: Could not detect a compiler on local system
which can compile the specified input file(s)
Error using RegionGrowing (line 67)
Could not compile the mex file :(. Please try to do so manually!

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28 Apr 2014 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin syed umar

When I pressed run, i got this error :Please define one of the current images
Please tell me how to solve this as I am a bit new to matlab. Please help. Thank you.

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23 Apr 2014 Livewire (Intelligent Scissors) ROI Creation Implementation of the livewire algorithm for intelligent ROI drawing. Can be used instead of ROIPOLY Author: Christian Wuerslin Mehmet Erdem

thanks for the great program. But after i plant seeds (or anchors), the output is the background. What should I do to get the extracted part?

5
18 Apr 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Charles

5
10 Apr 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin t zq

t zq (view profile)

great!

5
08 Apr 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Christian Baumgartner

I really enjoy working with your submission. Works perfectly, easy to understand and really nice UI. Well done!

5
02 Apr 2014 Dicom Import GUI Sorts DICOM files into series and lets you select the series you want to load in a GUI Author: Christian Wuerslin Brent Foster

5
02 Apr 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Trung

Trung (view profile)

Sorry, I have figured it out. Holding right mouse button or using "Ctrl + left mouse" would allow the zoom function.

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02 Apr 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Trung

Trung (view profile)

This is a great app. However, I am unable to zoom. Is there anyone having the same problem or how can I zoom my imported images in the GUI of this app?

5
05 Mar 2014 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin Michael Völker

This is well done!

I have a minor suggestion for the visualization of the result (nargout == 0). For large No. of slices in a 3D data set, the output of montage() is very hard to grasp. My suggestion is to present only image slices that are part of the segmented volume:

Below line 89, add
% reduce montage size by selecting the interesting slices, only
slices = squeeze( sum(sum( dMask(:,:,1,:) ,1),2) > 0 );

And change line 90 to:
figure, montage(dImg(:,:,:,slices));

5
26 Feb 2014 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Ta Hai

Ta Hai (view profile)

nice job! thank you

5
23 Dec 2013 Dicom Import GUI Sorts DICOM files into series and lets you select the series you want to load in a GUI Author: Christian Wuerslin Earl DuBack

When I run apple version, I get figure consisting of 3 images because there are 3 sets of DICOM images. The text "Dicom Import [press enter to confirm] is there. The number of images in each set is 74,74,28. I suspect the figure is supposed to have all thumbnails in a set behind one another? that I am supposed to be able to move through using mouse or up/down arrow keys. BUT figure is frozen with no way to view any other images in set.
EARL

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16 Dec 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin francesco

very great tool, either more interactive! :)

5
04 Dec 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Tobias Haushahn

5
02 Dec 2013 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin Maxim

Maxim (view profile)

5
23 Sep 2013 Dicom Import GUI Sorts DICOM files into series and lets you select the series you want to load in a GUI Author: Christian Wuerslin Matt J

Matt J (view profile)

Seems to work pretty well!

Just as a minor thing, it would be nice if the GUI had a scroll bar to move among the different series and to see better where you are within the list.

5
23 Sep 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Michael

5
24 May 2013 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin Christian Wuerslin

Hi Chris,

actually there is nothing really new in this algorithm. I only decided to trade a little bit of accuracy for a lot of speed. This is done by using the differen queues which can be regarded as intensity difference bins. I saw a similar approach in a paper by Johan Berglund (2010 in "Magn Reson Imaging") in a slightly differen context, however, I do not know whether he came up with it himself.

Christian

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23 May 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Martin

Martin (view profile)

5
23 May 2013 Fast 3D/2D Region Growing (MEX) A very fast 2D and 3D region growing algorithm implemented in c++. Author: Christian Wuerslin Chris Walker

Nice work Christian. Did you develop the algorithm yourself? Will it appear as a published article?
Chris W

5
05 May 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Paul Andrews

4
01 May 2013 Livewire (Intelligent Scissors) ROI Creation Implementation of the livewire algorithm for intelligent ROI drawing. Can be used instead of ROIPOLY Author: Christian Wuerslin Valeria Marin

buen material

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18 Apr 2013 Livewire (Intelligent Scissors) ROI Creation Implementation of the livewire algorithm for intelligent ROI drawing. Can be used instead of ROIPOLY Author: Christian Wuerslin Jehan Ziad Ghafuri

5
12 Apr 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Arindam Bose

Arindam Bose (view profile)

5
06 Apr 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Christian Wuerslin

Hi Jiro,

OK, I think I'm starting to get the idea of the difference between app and function :). So the next version of the app will simply return the figure handle to comply with the specs.

Thanks for the publicity <3

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05 Apr 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Jiro Doke

Jiro Doke (view profile)

Yes, I think what you're doing makes sense if people are using your app from the command line. The App, on the other hand, is used through the Apps tab, so there won't be a use case of having an output argument anyway. Because of that, I think you can just remove that capability when packaging.

Great tool. BTW, I highlighted your entry on the File Exchange Pick of the Week:

http://blogs.mathworks.com/pick/2013/04/05/3d-image-viewer/

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05 Apr 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Christian Wuerslin

Hi Jiro,

wow, thanks for the thorough investigation. Would have taken me forever to figure that out. Well, I was trying to give people the possibility to add arbitrary plots (e.g. quiver, lines) to the axes and thus introduced the axes handle output. Since the axes are destroyed when the panel leyout is changed, I disabled this feature when the axes handles are returned. I guess I have to think of something different for the app. Thanks for your suggestions!

Cheers,

Christian

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04 Apr 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Jiro Doke

Jiro Doke (view profile)

Christian,

I think I know what's going on. When you create an App, MATLAB checks to see if your function has an output argument or not. If it does, it will call "imagine" with an output argument. I see that in your code, you disable the ability to change the number of axes when "nargout" is 1.

Just as a note: as you can see from the documentation for Apps (the Tips section)

http://www.mathworks.com/help/matlab/creating_guis/app-creation.html

MATLAB assumes that the output from your function is a figure handle, and that's how it detects whether the figure has closed or not.

A fix would be to use a slightly different version of "imagine" for the App version, and not disable the multi-axes option. You can also output the handle of the figure, as opposed to the handle of the axes.

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04 Apr 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Christian Wuerslin

Hi Jiro,

thanks for the feedback and making me aware of the bug. I can't test it at the moment and I am a bit puzzled why this error ocurres since the app uses the same m-file as the normal submission, which works fine (at least for me). I'll fix it as soon as I get to my 2012b workstation.

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03 Apr 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Jiro Doke

Jiro Doke (view profile)

Great tool, Christian!

I noticed that the App version has the "Panel Layout" button disabled, and I can't change the layout to show multiple frames.

I really like the interface and the look&feel of the App!

5
27 Feb 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Ronald

Ronald (view profile)

5
25 Feb 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Christian Wuerslin

Hi Roland,

concerning the error: I must have accidentially changed the name of the subfolder "EvalFucntions" to "EvalFunctionsf". Rename this folder and it should work; I will also upload a fixed version asap.

The slice number is shown in the upper left corner of each image panel (since the panels might show different slices) togehter with the total number of slices.

To put the tooltip in the upper left corner is a good idea, I will incorporate that.

Thanks for your feedback!

Christain

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25 Feb 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Ronald

Ronald (view profile)

Nice submission!
I encountered one error, Imagine cannot use the find the fEvalLineFWHM function (it is not on the path). Should be easy to fix.

Also some nice additions would be:
- show a tooltip for the buttons (or a text at the location where not the position and pixel value is shown).
- add the slice position instead of only showing x and y.

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22 Feb 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Thomas

Thomas (view profile)

Best MRI image visualization tool!

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22 Feb 2013 Imagine 4D/3D image visualization and evaluation GUI. Author: Christian Wuerslin Thomas

Thomas (view profile)

5

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