[Insight-users] Image Series Order - itk::ImageSeriesReader, SetReverseOrder

[Luke Bloy]

Hi Luis,

I'm now confused by the difference between itk::Image and
itk::OrientedImage. I thought the itk::Image had the ability to encode
the Orientation in directions variable. Is that not the case? what does
itk::OrientedImage offer that itk::Image doesn't?

I've also noticed that all the fileWriters seem to convert output images
to the LPS frame. Is that true? Is it configurable?

thanks.
Luke


On Tue, 2008-07-08 at 15:23 -0400, Luis Ibanez wrote:
> Hi Michael,
> 
> 
>                  Welcome to ITK !
> 
> 
> Thanks for the detailed description of your problem.
> 
> With that, you are starting with a good precedent  :-)
> 
> 
> If you are finding necessary to play with the order of
> reading the DICOM slices in order to get the anatomical
> orientation of the images to match, then chances are that
> the image have been acquired with different orientations.
> 
> The good news for you is that ITK provides classes for
> correctly taking image orientation into account.
> 
> 
> What you want to do first is to replace the use of
> "itk::Image" in your code, with "itk::OrientedImage".
> 
> 
> The OrientedImage will make sure that the image orientation
> that is encoded in the direction cosines stored in the
> DICOM header, is propagated and taking into consideration
> at every step of the image registration process.
> 
> 
> Once you introduce the itk::OrientedImage in replacement
> for the itk::Image, you shouldn't need to manipulate the
> slice order in the ImageSeriesReader class.
> 
> 
> Note that for this,
> You should use ITK 3.6 or a later CVS version.
> 
> 
> Please give it a try and let us know if you find any
> problems.
> 
> 
> 
>     Thanks
> 
> 
>        Luis
> 
> 
> 
> -------------------
> M. Wirtzfeld wrote:
> > 
> > Good afternoon,
> > 
> > We are currently writing registration code to handle mono-modality and 
> > multi-modality image registration using CT and MR data-sets.
> > 
> > At the present time, the code is able to perform registration using both 
> > of these data-sets.  The fixed-image is two-dimensional (treated as 
> > three-dimensional image-type by the code) and the moving-image is a 
> > volume created from a sequence of two-dimensional DICOM slices.
> > 
> > Using the itk::ImageSeriesReader class, mono-modality CT registration 
> > requires the SetReverseOrder method of this class to be called with a 
> > "true" boolean value and MR registration requires a "false" boolean 
> > value when the respective volumes are created.
> > 
> > I have ensured that the maximum-step used by the optimizer is properly 
> > set in both cases.
> > 
> > I believe the root of this requirement lies in the meta-data of the 
> > DICOM images that comprise the CT and MR data-sets, but I do not know 
> > why or what to look for in order to help find an answer.
> > 
> > I have not used ITK extensively and this is my first experience with 
> > image-processing.
> > 
> > 
> > 
> > Any help is greatly appreciated,
> > 
> > 
> > Michael.
> > 
> > Michael Wirtzfeld
> > Robarts Research
> > 
> > "Prefer the standard to the offbeat." - Strunk & White
> > 
> > 
> > ------------------------------------------------------------------------
> > 
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