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

[Baoyun Li]

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>
To: Luis Ibanez <luis.ibanez at kitware.com>
Cc: 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



      
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