I did slice extraction once. The code was posted on this list some months ago. Take a look there.<br><br>You should set input image once, before the loops. You should not call disconnect at all.<br>In loops, call setExtractionRegion, update and getOutput.<div>
<br>In the code excerpt you provided, you never initialize the variable gsquare_size. It should be initialized before the loops, if it is not already so.</div><div><br></div><div>I didn't know before that there exist "<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">UpdateLargestPossibleRegion" :D</span><br>
<div><font class="Apple-style-span" face="verdana, sans-serif"><br></font><div class="gmail_quote">On Tue, Aug 9, 2011 at 19:48, Kevin Zhang <span dir="ltr"><<a href="mailto:zhangk@uchicago.edu">zhangk@uchicago.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello all,<br>
<br>
I am attempting to implement a grid-based thresholding algorithm over a 3D image volume. I am trying to use ExtractImageFilter to extract 2D square subregions from each slice in the volume. Code is as follows:<br>
<br>
ExtractFilterType::Pointer ExtractSquareFilter = ExtractFilterType::New();<br>
for(unsigned int i = 0; i < numslices; i++)<br>
{<br>
// extract grid square, iterating across row and column of slice<br>
for(unsigned int sr = 0; sr < num; sr++)<br>
{<br>
for(unsigned int sc = 0; sc < num; sc++)<br>
{<br>
FloatImageType::RegionType gsquare_region;<br>
FloatImageType::RegionType::<u></u>IndexType gsquare_index;<br>
gsquare_index[0] = sc * sidelength;<br>
gsquare_index[1] = sr * sidelength;<br>
gsquare_index[2] = i; // set slice<br>
gsquare_region.SetSize(<u></u>gsquare_size);<br>
gsquare_region.SetIndex(<u></u>gsquare_index);<br>
ExtractSquareFilter->SetInput(<u></u>inputimg);<br>
ExtractSquareFilter-><u></u>SetExtractionRegion(gsquare_<u></u>region);<br>
ExtractSquareFilter-><u></u>UpdateLargestPossibleRegion();<br>
Float2DImageType::Pointer square = ExtractSquareFilter-><u></u>GetOutput();<br>
square->DisconnectPipeline();<br>
std::cerr << "Grid square extracted successfully" << std::endl;<br>
<br>
The input dataset is a series of 128x128 images. I am currently trying to divide each slice into a 4x4 grid, where each square would be 32x32.<br>
<br>
The errors I get when executing are:<br>
itkImageConstIteratorWithIndex<u></u>.txx:90: itk::<u></u>ImageConstIteratorWithIndex<<u></u>TImage>::<u></u>ImageConstIteratorWithIndex(<u></u>const TImage*, const typename TImage::RegionType&) [with TImage = itk::OrientedImage<float, 2u>]: Assertion `Region ImageRegion (0xbf7ff6ec)<br>
Dimension: 2<br>
Index: [0, 0]<br>
Size: [32, 32]<br>
is outside of buffered region ImageRegion (0x97d3680)<br>
Dimension: 2<br>
Index: [32, 0]<br>
Size: [32, 32]<br>
' failed.<br>
<br>
I have tried several things to fix this, including:<br>
1. Instantiate the ExtractImageFilter inside the loop<br>
2. Use UpdateLargestPossibleRegion() instead of Update() on ExtractImageFilter<br>
<br>
Thanks in advance for any insights! No pun intended.)<br>
<br>
Kevin Zhang<br>
Student Research Assistant<br>
Department of Radiology / Cancer Research Center<br>
University of Chicago<br>
<br>
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