[ITK-users] Error encountered when padding: boundary condition is ITK_NULLPTR

[Matt McCormick]

Hi Marie,

Is getBounds() returning physical coordinates or index coordinates?
PadImageFilter uses index coordinates.

Here is an example:

  https://itk.org/ITKExamples/src/Filtering/ImageGrid/PadAnImageWithAConstant/Documentation.html

Hope this helps,
Matt

On Tue, Aug 29, 2017 at 6:56 AM, avazuila <mbrunet at insa-rennes.fr> wrote:
> Hi all,
>
> I just performed the segmentation of a vessel from a CT scan and I would
> like to use it to mask the abovementioned vessel on the image. In order to
> do so I would like to pad the segmentation image which is smaller than the
> image from which it has been extracted.
>
> I get the following error: "PadImageFilter: Boundary condition is
> ITK_NULLPTR so no request region can be generated."
>
> My code is the following:
>
> double* voi_bounds = l_import_preprocess.getBounds();
> double* seg_bounds = l_import_seg.getBounds();
>
> double x_min = abs(voi_bounds[0] - seg_bounds[0]);
> double x_max = abs(voi_bounds[1] - seg_bounds[1]);
> double y_min = abs(voi_bounds[2] - seg_bounds[2]);
> double y_max = abs(voi_bounds[3] - seg_bounds[3]);
> double z_min = abs(voi_bounds[4] - seg_bounds[4]);
> double z_max = abs(voi_bounds[5] - seg_bounds[5]);
>
> const int Dimension = 3;
> typedef uchar PixelType;
> typedef itk::Image< PixelType, Dimension > ImageType;
>
> ImageType::SizeType upper;
> ImageType::SizeType lower;
>
> lower[0] = x_min;
> lower[1] = y_min;
> lower[2] = z_min;
>
> upper[0] = x_max;
> upper[1] = y_max;
> upper[2] = z_max;
>
> typedef itk::PadImageFilter< ImageType, ImageType > PadFilterType;
> PadFilterType::Pointer l_pad = PadFilterType::New();
> l_pad->SetInput(l_import_seg.getOutput());
> l_pad->SetPadUpperBound(upper);
> l_pad->SetPadLowerBound(lower);
>
> typedef itk::ImageFileWriter< ImageType > WriterFilterType;
> WriterFilterType::Pointer l_writer = WriterFilterType::New();
> l_writer->SetInput(l_pad->GetOutput());
> l_writer->SetFileName(logDir.toStdString() + "voi.mhd");
> try{
>         l_writer->Update();
> }
> catch (itk::ExceptionObject& err) {
>         M_Error(String(err.what()));
> }
>
> I also tried to crop the original image to make it fit the segmentation
> dimensions but it always is a few pixels smaller than the segmentation image
> and I have no idea why. Moreover, this gap is never the same and seems to be
> proportional to the segmentation image size.
>
> Why can't I perform the padding of my segmentation image?
> Plus, does anybody know why I can't crop the original image without having a
> few pixels less than needed?
>
> Thanks in advance,
>
> Marie
>
>
>
> --
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