3D FFT problem

[Mariam Dost]

Hi,

I'm having troubles getting a 3D FFT by using ICY. I installed all the plugins but when I click to make a 3D image, the program gets stuck and does not produce any image at all, instead just an empty grid. I am opening .dcm (dicom) images into the program and the 2D FFT that is computed by ICY is quite different from the one computed by ImageJ. Does anybody know why, or am I just doing this wrong. 

Thanks. 

[Alexandre Dufour]

Hi Mariam,

I can only make a few guesses, but may be you might find a solution;

 - the FFT plugin outputs a 2-channel image wither real/imaginary or amplitude/phase representation. Make sure you select the latter (as ImageJ does, but only showing you the amplitude as far as I remember)

 - FFT spectra potentially have a high dynamic range, therefore the display is skewed to fit your screen. However their log-view are easier to see. Make sure you use the "Log2D" viewer to look at your output, and of course top-up with contrast adjustment if need be. 

I would presume the same thing happens (perhaps worse so) in the 3D case, so have try on both cases and let us if something looks clearly strange. 

Alexandre

--
You received this message because you are subscribed to the Google Groups "Icy imaging" group.
To unsubscribe from this group and stop receiving emails from it, send an email to icy-software...@googlegroups.com.
To post to this group, send email to icy-so...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/776c92a2-2e79-403b-8899-4605dd287930%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Mariam Dost]

Hi,

I tried doing as you said but the problem still is the same. I have attached a screenshot on what the FFT looks like. I don't what I am doing wrong. 

Thanks.

[Alexandre Dufour]

Hi Mariam,

You are almost there! Just a few more things:

 - You should check the “swap quadrants” option: by default the lowest magnitude lands on pixel (0,0), which is the default for mathematical operations in the Fourier domain. But for visualisation purposes swapping the quadrants will place the lowest frequency in the center of the image, where you can actually see something…

 - The phase information (in green) is significantly more varied (and harder to interpret, but that’s another story), and therefore it skews the visualisation so much that the magnitude (in red) isn’t visible anymore (although it’s there). All you have to do know is “hide” the phase channel, by unchecking the green channel in the sequence panel of the inspector. You should be left with the magnitude (in red), which you can change to another color or pseudo color to make it look nicer.

I do notice however a strange behaviour in the Log2D viewer (doesn’t seem to work all the time), so I will have a look into it, but in the meantime you should still be able to see the magnitude by shifting the contrast bars a bit:

Alexandre

To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/6dd92d31-591c-436a-9d2e-c72c4093b4fb%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

<Screen Shot 2014-07-16 at 10.39.45 AM.png>

[Mariam Dost]

Hi,

Thanks I got the image now. But how do you get the image to be displayed in 3D? Cause when I click 3D all I get is an empty grid. Does it not work on the image I have?

[Alexandre Dufour]

On my screenshot the image was 2D, so obviously the 3D view would not have worked, but here is a screenshot of the 3D version of the MRI stack. Notice how I have adjusted the contrast bars to see the spectrum a bit better.

However, if with the same viewer settings you are still not seeing anything, try deactivating some of the 3D widgets (box, grid, axes, etc.), as I have noticed that in rare occasions this could fix the problem. 

And as a final note, make sure you are using preferably a 64-bit OS (that should be standard by now) and especially a 64bit version of Java (you can check this when Icy starts up, in the console panel). The 64-bit version is generally more stable, and especially when it comes to 3D (again, based on past experience).

Alexandre

To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/43d8c48b-d771-442c-ba61-d6012d2f379e%40googlegroups.com.