[Insight-users] Extract 2D slice put back as 3D correct orientation

[Bradley Lowekamp]

Hello,

I think the TileImageFilter may do what you want:

http://www.itk.org/Doxygen/html/classitk_1_1TileImageFilter.html

http://www.itk.org/Wiki/ITK/Examples/ImageProcessing/TileImageFilter_CreateVolume

I think if you specify a [ 0, 1, 1 ] layout with just your one image it should do the trick.

Brad

On Apr 30, 2013, at 6:35 PM, Emma Saunders <emmasaunders123 at gmail.com> wrote:

> Hi Bradley thanks for you help.  This doesn't appear however to satisfy what I need.  I have a 2D sagittal slice in 3D form with dimensions [1 128 128] with RAI orientation as defined in ITK snap.  I permute the axis as you suggested to give [128 128 1].  I then use extract image filter to get the 2D slice and perform some processing.  I would then like to put the 2D slice back into it's original form, I therefore use cast Image filter to again make it a 3D image, I then permute once again to get [1 128 128] dimensions, this however changes the orientation to another form and will not allow me to reproduce the original image.  Is there something Im missing?
> 
> Thanks for your help
> 
> Emma
> 
> 
> On Tue, Apr 30, 2013 at 8:18 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello Emma,
> 
> Perhaps the PermuteAxesImageFilter will help you:
> 
> http://www.itk.org/Doxygen/html/classitk_1_1PermuteAxesImageFilter.html
> 
> Brad
> 
> On Apr 30, 2013, at 2:46 PM, Emma Saunders <emmasaunders123 at gmail.com> wrote:
> 
> > Hi everyone,
> >
> > I'm struggling with what I should imagine should be quite simple.  I extract a slice from a 3D volume [128,128,128] along it's first dimension, thus setting the size[0]=0;
> >
> > I would like to then put this back into the 3D volume but the orientation is incorrect when using cast Image filter to load back as a 3D as it only saves it as a transaxial slice in the volume, not a sagittal.  I have attempted re-orienting the direction cosines of the images but this just laves me with an image with a different orientation, what I would like is to somehow switch the pixel values in a given dimensions from [1 128 128] to [128 128 1]?
> >
> > Any help appreciated?
> >
> > Kind regards
> >
> > Emma
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