[Insight-users] Istropic resampled CT image got fipped at y direction, and out of range

[Luis Ibanez]

Hi Baoyun,

Thanks for letting us know that this fixed the problem.

We have now added the SetOutputDirection() call to all
the other resampling examples in the directory:

           Insight/Examples/Filtering



   Regards,


      Luis


---------------------
Baoyun Li wrote:
> Luis:
>  
> Thank you so much. Now the output is correct.
>  
> Best Regards
>  
> Baoyun
> 
> ------------------------------------------------------------------------
> *From:* Luis Ibanez <luis.ibanez at kitware.com>
> *To:* Baoyun Li <baoyun_li123 at yahoo.com>
> *Cc:* insight-users at itk.org
> *Sent:* Friday, February 20, 2009 11:41:59 AM
> *Subject:* Re: Istropic resampled CT image got fipped at y direction, 
> and out of range
> 
> Hi Baoyun,
> 
> 
>     Congratulations !
> 
>     You just found a bug in the ITK Example.
> 
> 
> 
> The Example is missing to call the method
> 
>       SetOutputDirection()
> 
> a fix has been committed to CVS
> http://www.itk.org/cgi-bin/viewcvs.cgi/Examples/Filtering/ResampleVolumesToBeIsotropic.cxx?root=Insight&r1=1.21&r2=1.22&sortby=date 
> <http://www.itk.org/cgi-bin/viewcvs.cgi/Examples/Filtering/ResampleVolumesToBeIsotropic.cxx?root=Insight&r1=1.21&r2=1.22&sortby=date>
> 
> Simply try adding the line:
> 
>   resampler->SetOutputDirection( inputImage->GetDirection() );
> 
> 
> just after:
> 
>   resampler->SetOutputOrigin( inputImage->GetOrigin() );
> 
> 
> Without this line, the filter is setting the direction of the
> output image to be an identity matrix (direction cosines),
> while, most likely, your in put image has a different type
> of direction.
> 
> You can always verify this by adding a print out:
> 
> 
>     std::cout << inputImage->GetDirection() << std::endl
> 
> 
> --
> 
> 
> Please let us know if you still see any problem,
> 
> 
>   Thanks
> 
> 
>       Luis
> 
> 
> -------------------
> Baoyun Li wrote:
>  > Dear All:
>  > This is regarding to yesterday's email, resampled image got out of 
> range values for all voxel.
>  > I am trying to resice the CT data to Isotropic, and the program I am 
> using is ResampleVolumesToBeIsotropic.cxx for the ITK filter example.
>  >  Now I  remove this :
>  > resampler->SetOutputOrigin( inputImage->GetOrigin() );
>  >  and reader: origin1=inputImage->GetOrigin(),
>  >  the value for origin1 are all [0 0 0];
>  >  1 if we set origin2=[0 0 0] and  resampler->SetOutputOrigin(origin2),
>  >  I got all zeros value on the output image.
>  >  2 if I set origin2=[0 -300 0], we saw most part of the CT image, but 
> the image is fippled at top down direction from MRICro.
>  >  my input and out put are all hdr file, I tried nii data and have the 
> same problem
>  >  Can somebody tell me how to solve the problem?
>  >  Baoyun
>  >
>  > ------------------------------------------------------------------------
>  > *From:* Baoyun Li <baoyun_li123 at yahoo.com 
> <mailto:baoyun_li123 at yahoo.com>>
>  > *To:* Luis Ibanez <luis.ibanez at kitware.com 
> <mailto:luis.ibanez at kitware.com>>
>  > *Cc:* insight-users at itk.org <mailto:insight-users at itk.org>
>  > *Sent:* Thursday, February 19, 2009 4:53:30 PM
>  > *Subject:* error when resampling the CT data to Isotropic
>  >
>  >
>  > Dear All:
>  >  I am trying to resice the CT data to Isotropic, and the program I am 
> using is ResampleVolumesToBeIsotropic.cxx for the ITK filter example.
>  >  My input data is called SE1.hdr
>  > the space resolution is 0.7*0.7*2.5.
>  >  After I run the program, I got the output.hdr. The number of voxels 
> and the spacing of the output are correct after I check the result at 
> MRICro. But all the voxel has the default outside value. Seems after the 
> indentity transform, all the voxels are out of range.
>  >  Also I output  the SmootherY results, it is ok.
>  >  Can any body let me know what happend? How to check the value of 
> transform.
>  >  /////////////////////////////changes I made on the code
>  > typedef  short  InputPixelType;
>  >  intensityWindowing->SetOutputMinimum(  0.0 );
>  >  intensityWindowing->SetOutputMaximum( 1200.0 ); // floats but in the 
> range of chars.
>  > typedef  short  OutputPixelType;
>  >  and some writers to record the interval output.
>  >  ////////////////////////
>  >  I also checked the results using NII as input and output, the 
> resliced image contains all background value. I doubt the problem 
> happend at the
>  >  typedef itk::IdentityTransform< double, Dimension >  TransformType;
>  >  TransformType::Pointer transform = TransformType::New();
>  >  transform->SetIdentity();
>  >  resampler->SetTransform( transform );
>  >  Can somebody help me to figure out this problem??
>  >  Thanks
>  >  Baoyun
>  >
>  >
>