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

[Alexandre GOUAILLARD]

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 <http://mc/compose?to=chyumm@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<http://mc/compose?to=dzenanz@gmail.com>
> >* wrote:
>
>
> From: Dženan Zukić <dzenanz at gmail.com<http://mc/compose?to=dzenanz@gmail.com>
> >
> Subject: Re: [Insight-users] How ITK handles non-equal spacing images
> To: "Jay Li" <chyumm at yahoo.com <http://mc/compose?to=chyumm@yahoo.com>>
> Cc: insight-users at itk.org <http://mc/compose?to=insight-users@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<http://mc/compose?to=chyumm@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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