Use of Slicer2.6 as a workaround for Slicer3 3.5 3D volume view

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Use of Slicer2.6 as a workaround for Slicer3 3.5 3D volume view

madanrao
Hello,

I am giving an example of a common problem in Slicer3 3.4/3.5 (that I was facing) and its solution here.

I have a dicom image set: 512 x  512 x 119, spacing: 0.46785, 0.46785, 1.5, Origin: -119.77, -119.77,-269.5.

The 3D image is outside the 3D box in Conventional layout. This gives several problems for example in tumor segmentation
or vascular modelling.

If we change the values of image origin we are supposed to get a correct view. However, it is impractical since we do not know
how to randomly change these values.

While working on a solution I happen to find that Slicer2.6-opt-win32-x86-2006-08 not only can open 3D view correctly but also
report any errors. In other words, Slicer2.6 can find the correct values of the Origin for us. When I tried to save the image as *.nhdr
file, I got a memory overload error. I converted the dicom images to raw using mcverter and reloaded and saved as *.nhdr files.

The correct values that load the 3Dview of the image are: 119.77, 119.77, 88.5.

Hope this helps.

AM Mohan Rao



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Re: Use of Slicer2.6 as a workaround for Slicer3 3.5 3D volume view

Dominik Meier
Since Slicer operates in mm space, the default center is the image  
center (half the dimensions) times the voxel size, i.e.
[0.46785, 0.46785, 1.5] .* [512 512 119] / 2 =  119.77, 119.77, 88.5.

There is a "Center Volume" button in the "Volumes" module. You should  
be able to change the Image Origin data directly.

Dominik

On Feb 3, 2010, at 9:19 AM, Madan Rao wrote:

> Hello,
>
> I am giving an example of a common problem in Slicer3 3.4/3.5 (that  
> I was facing) and its solution here.
>
> I have a dicom image set: 512 x  512 x 119, spacing: 0.46785,  
> 0.46785, 1.5, Origin: -119.77, -119.77,-269.5.
>
> The 3D image is outside the 3D box in Conventional layout. This  
> gives several problems for example in tumor segmentation
> or vascular modelling.
>
> If we change the values of image origin we are supposed to get a  
> correct view. However, it is impractical since we do not know
> how to randomly change these values.
>
> While working on a solution I happen to find that Slicer2.6-opt-
> win32-x86-2006-08 not only can open 3D view correctly but also
> report any errors. In other words, Slicer2.6 can find the correct  
> values of the Origin for us. When I tried to save the image as *.nhdr
> file, I got a memory overload error. I converted the dicom images  
> to raw using mcverter and reloaded and saved as *.nhdr files.
>
> The correct values that load the 3Dview of the image are: 119.77,  
> 119.77, 88.5.
>
> Hope this helps.
>
> AM Mohan Rao
>

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