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<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Hi,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>It seems I’m a bit confused about the
ExtractImageFilter. I’m trying to use it to extract a slice from a 3D
image, so far so good. However when I use the extracted slice as input for
ResampleImageFilter I seem to be getting into trouble (that is: garbage
output).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>After some debugging I got confused about the
following: the ExtractImageFilter does not recomputed the origin (apparently
this is intended) and consequently the image index is set to the index
corresponding to the extraction region. So if I want to extract slice 10 and
use index=(0,0,10) then the index of the regions of the output image is
(0,0,10) as well. However, and this is the confusing part for me, the size of
the output image will be (256,256,1). That is, the index extends beyond the
maximum allowed image. How should I deal with this?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Best,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>Jeroen<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-US style='font-size:
10.0pt;font-family:Arial'>This is a code snippet where I’m trying to
extract a slice and then super-sample it:<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>void</span></font>
SlabExtractionFilter::GenerateData ()<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> {<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=blue><span style='color:blue'>const</span></font> Image *inputImage =
GetInput ();<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> m_Extracter->SetInput
( inputImage );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=green><span style='color:green'>m_Extracter->SetExtractionRegion (
slabRegion ); // selects a slice from the volume<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'>
m_Resampler->SetOutputDirection ( inputImage->GetDirection () );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> m_Resampler->SetOutputOrigin
( outputOrigin ); // the origin belonging to the extracted slice <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> m_Resampler->SetOutputSpacing
( outputSpacing ); // one-third of the spacing in the z-dimension of the input
image<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'>
m_Resampler->SetSize ( outputSize ); // 256,256,3<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> m_Resampler->SetInput
( m_Extracter->GetOutput () );<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> <font
color=green><span style='color:green'>//m_Resampler->GraftOutput (
this->GetOutput () );<o:p></o:p></span></font></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
lang=EN-GB style='font-size:10.0pt;font-family:"Courier New"'> </span></font><font
size=2 face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New"'>m_Resampler->Update
();<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'> GraftOutput ( m_Resampler->GetOutput () );<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'> }</span></font><font size=2 face=Arial><span
lang=EN-US style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
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