[Insight-users] How ITK handles non-equal spacing images

[Jay Li]

Hi Alex,

Thank you very much for your suggestion. 

Regards,
Jay

--- On Sat, 8/14/10, Alexandre GOUAILLARD <agouaillard at gmail.com> wrote:

From: Alexandre GOUAILLARD <agouaillard at gmail.com>
Subject: Re: [Insight-users] How ITK handles non-equal spacing images
To: "Jay Li" <chyumm at yahoo.com>
Cc: "Dženan Zukić" <dzenanz at gmail.com>, insight-users at itk.org
Date: Saturday, August 14, 2010, 4:46 PM

hi,
You definitly want to work in 3D.
You can either check the filters that support he spacing information with your original dataset (my wild guess is that most recent filters like Chan and Vesse level set should),
or resample your 3D image to get an isotropic image.
regards,
alex.

2010/8/14 Jay Li <chyumm at yahoo.com>

Hi Dženan,

I appreciate your suggestions/answers. Thank you very much. It's really helpful.


Regards,
Jay

--- On Fri, 8/13/10, Dženan Zukić <dzenanz at gmail.com> wrote:


From: Dženan Zukić <dzenanz at gmail.com>
Subject: Re: [Insight-users] How ITK handles non-equal spacing images
To: "Jay Li" <chyumm at yahoo.com>

Cc: insight-users at itk.org
Date: Friday, August 13, 2010, 3:28 AM

Hi Jay!
That approach is called 2.5D. It was common 10-15 years ago, but it is no longer common because you basically ignore information using it. I also deal with similarly anisotropic images (0.625 in x and y, 4.4 in z). And yes, low Z resolution is a pain in the butt,
 but if you restrict yourself to sequence of 2D slices, good results become harder to achieve.


But reading your arguments, I can see the point - I haven't given it much thought until now. And I don't consider myself to be an expert either.
Regards,Dženan




2010/8/13 Jay Li <chyumm at yahoo.com>




Hi Dženan,

Thanks for your input. I'm hoping to get a feeling on how to choose appropriate algorithms/filters for 3D non-equal spacing images in general. I was told that it would be more appropriate to perform 2D filters than 3D filters to the image I described in the first email (0.2 mm spacing along x, y, 1 mm spacing along z), because the spacing in z direction is five times of it along x and y. As I'm not an expert in image processing, I don't know if this is a common approach in the industry. I'm kind of hoping experts on this forum could give me some insights. Thank you again.





Regards,
Jay

--- On Tue, 8/10/10, Dženan Zukić <dzenanz at gmail.com> wrote:





From: Dženan Zukić
 <dzenanz at gmail.com>
Subject: Re: [Insight-users] How ITK handles non-equal spacing images
To: "Jay Li" <chyumm at yahoo.com>




Cc: insight-users at itk.org
Date: Tuesday, August 10, 2010, 9:12 AM

Hi Jay,
ITK image has support for different spacings along each axis, unfortunately not all filters take this information into account (most should though). The best way to check is to take a look at the source code.






Regards,Dženan

On Tue, Aug 10, 2010 at 02:54, Jay Li <chyumm at yahoo.com> wrote:






Dear ITK Users,
 
I have a question regarding how ITK handles images with non-equal spacings in general. For example, I have a 3D volume with the spacing of 0.2 mm along X and Y axis respectively, but 1 mm spacing in Z direction. If I apply a 3-D level set segmentation algorithm to the image, is this going to be a concern due to the larger spacing in Z direction? Or instead should I try 2-D  level set segmentation slice by slice on X-Y plane? Any suggestion is appreciated. Thank you.






 
Regards,
Jay


      
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