[Insight-users] Slice thickness

[Andinet Enquobahrie]

Olivier Rousseau wrote:

> Hi,
>
> I have created a 3D image from 2D slices using "RGBImageSeriesReadWrite".
> It seems that by default, the filter has set the thickness of the 
> slices to be 1mm,
> but the slices I am using are 0.33mm thick. I tried to change the 
> thickness
> directly in the header, but the image is so big (500Mb), that I can't 
> open it in any
> text editor.
> Is there a way to either change the header within ITK, or specify the 
> thickness
> when I run "RGBImageSeriesReadWrite"?
>
> Thanks for your help!!

Hello Olivier,

First of all, I am not sure why you are using "RGBImageSeriesReadWrite" 
to generate a volume (3D) from a series of 2D slices. You should be using
the "ImageSeriesReadWrite.cxx" code in the same directory 
(Insight/Examples/IO).

Second, what format are your writing out your volume? You can write it 
out in MetaImage format and then edit the header (*.mhd). In the header, 
there is an
an entry for element spacing.. For example, here is a typical image 
header format

 NDims = 3
 DimSize = 181 217 181
 ElementType = MET_UCHAR
 ElementSpacing = 1.2   1.2   3.4
 Offset = 13.4  27.5  43.2
 ElementByteOrderMSB = False
 ElementDataFile = brainweb1.raw


For more information on MetaImage format, refer to
http://www.itk.org/HTML/Data.htm

-Andinet


> Olivier
>
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