[Insight-users] Convert a set of 2D images to 3D
Bradley Lowekamp
blowekamp at mail.nih.gov
Wed Apr 29 16:25:44 EDT 2009
There is also the JoinSeriesImageFilter. Here is how I have used it
before:
typedef itk::JoinSeriesImageFilter<InputImageType, InputVolumeType>
JoinSeriesFilterType;
JoinSeriesFilterType::Pointer joinSeries =
JoinSeriesFilterType::New();
joinSeries->SetOrigin(inputOrigin[2]);
joinSeries->SetSpacing(inputSpacing[2]);
for (unsigned int z = 0; z < sliceTransforms.size(); ++z) {
typedef itk::ExtractImageFilter<InputVolumeType, InputImageType>
SlicerExtractorType;
SlicerExtractorType::Pointer sliceImageExtractor =
SlicerExtractorType::New();
SlicerExtractorType::InputImageRegionType
sliceSubRegion(inputVolume->GetLargestPossibleRegion());
sliceSubRegion.SetSize(2, 0);
sliceSubRegion.SetIndex(2, z);
sliceImageExtractor->SetExtractionRegion(sliceSubRegion);
sliceImageExtractor->SetInput(inputVolume);
sliceImageExtractor->Update();
... resampling of the slices...
joinSeries->PushBackInput(resample->GetOutput());
}
joinSeries->Update();
Hopefully one of the suggestions will work well for you.
Brad
On Apr 29, 2009, at 4:13 PM, Bill Lorensen wrote:
> Or you could use itkTileImageFilter. Note the last sentence in the
> documentation.
>
> /** \class TileImageFilter
> * \brief Tile multiple input images into a single output image.
> *
> * This filter will tile multiple images using a user-specified
> * layout. The tile sizes will be large enough to accommodate the
> * largest image for each tile. The layout is specified with the
> * SetLayout method. The layout has the same dimension as the output
> * image. If all entries of the layout are positive, the tiled output
> * will contain the exact number of tiles. If the layout contains a 0
> * in the last dimension, the filter will compute a size that will
> * accommodate all of the images. Empty tiles are filled with the
> * value specified with the SetDefault value method. The input images
> * must have a dimension less than or equal to the output image. The
> * output image have a larger dimension than the input images. This
> * filter can be used to create a volume from a series of inputs by
> * specifying a layout of 1,1,0.
> */
>
>
> On Tue, Apr 28, 2009 at 1:41 PM, Luis Ibanez
> <luis.ibanez at kitware.com> wrote:
>> Hi Luis,
>>
>> It is a bit more complicated than that.
>>
>> You will need to put the filter in a for loop,
>> where you iterate over all the slices.
>>
>> Inside the loop you take the output of the
>> PasteImageFilter and reconnect it as a new
>> input.
>>
>>
>> In Pseudo code it will look something like:
>>
>> ImageType::Pointer wholeImage;
>>
>> for-loop
>> {
>> pasteFilter->SetInput1( wholeImage );
>> pasteFilter->SetInput2( slice_i );
>> pasteFilter->Update();
>> wholeImage = pasterFilter->GetOutupt();
>> wholeImage->DisconnectPipeline();
>> }
>>
>>
>>
>> Regards,
>>
>>
>> Luis
>>
>>
>>
>> --------------------------
>> Luis Roberto P. Paula wrote:
>>>
>>> After that, all I need to do is to call the SetInput for each
>>> slice and,
>>> at the end, call the Update method?
>>>
>>> Thanks,
>>> Luis
>>>
>>> On Tue, Apr 21, 2009 at 10:06 AM, Luis Ibanez <luis.ibanez at kitware.com
>>> <mailto:luis.ibanez at kitware.com>> wrote:
>>>
>>>
>>> Hi Luis,
>>>
>>> You should instantiate the Paste filter in 3D.
>>>
>>> Since you are going to paste 2D slices into a 3D image,
>>> you need to set up the filter in such a way that a 2D
>>> image is seen as a 3D image of a single slice.
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>> Luis
>>>
>>>
>>> -----------------------------
>>> Luis Roberto P. Paula wrote:
>>>
>>> Hi Luis,
>>>
>>> I'm a little confused on how to use the itkPasteImageFilter.
>>>
>>> At first, I created the typedef:
>>>
>>> typedef itk::PasteImageFilter< ImageType2D > PasteFilter2D;
>>>
>>>
>>> Then:
>>>
>>> PasteFilter2D::Pointer paste2D = PasteFilter2D::New();
>>>
>>> // I'm lost in this part
>>>
>>> for (int i; i < VECTOR_SIZE; i++) {
>>> paste2D->SetInput( IMAGE2D_VECTOR[i] );
>>> }
>>>
>>> How do I make the output of the paste2D be a 3D image?
>>>
>>> Do I need to set to the destination image a 3D blank image?
>>>
>>> The destination index affects the output?
>>>
>>> I thought it would work like the add method of the std:vector
>>> class with an output as a 3D image, but it seems that it can
>>> return an image with the same dimension.
>>>
>>> Thanks,
>>> Luis
>>>
>>> On Fri, Apr 17, 2009 at 3:36 PM, Luis Ibanez
>>> <luis.ibanez at kitware.com <mailto:luis.ibanez at kitware.com>
>>> <mailto:luis.ibanez at kitware.com
>>> <mailto:luis.ibanez at kitware.com>>> wrote:
>>>
>>>
>>> Hi Luis,
>>>
>>> Yes,
>>> the same should work for pasting 3D images into to 4D
>>> images.
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>> Luis
>>>
>>>
>>> ---------------------------
>>> Luis Roberto P. Paula wrote:
>>>
>>> Thanks Luis!! This is a much better approach
>>> (itkPasteImageFilter).
>>>
>>> I guess it works the same way from 3D to 4D, right?
>>>
>>> Regards,
>>> Luis
>>>
>>> On Thu, Apr 16, 2009 at 1:59 PM, Luis Ibanez
>>> <luis.ibanez at kitware.com <mailto:luis.ibanez at kitware.com
>>> >
>>> <mailto:luis.ibanez at kitware.com <mailto:luis.ibanez at kitware.com
>>> >>
>>> <mailto:luis.ibanez at kitware.com
>>> <mailto:luis.ibanez at kitware.com>
>>> <mailto:luis.ibanez at kitware.com
>>> <mailto:luis.ibanez at kitware.com>>>> wrote:
>>>
>>>
>>> Hi Luis,
>>>
>>> If your images are in individual 2D files, then
>>> you could simply use the ImageSeriesReader.
>>>
>>> If your images are in an array of 2D images in
>>> memory, then you may want to use the Paste
>>> filter:
>>>
>>>
>>> http://itk.org/Doxygen/html/itkPasteImageFilter_8h.html
>>>
>>> You will have to call it multiple times...
>>> once per input slice.
>>>
>>>
>>> Regards,
>>>
>>>
>>> Luis
>>>
>>>
>>> ---------------------------
>>>
>>> Luis Roberto P. Paula wrote:
>>>
>>> Hi All,
>>>
>>> I have a set of 2D images in axial
>>> orientation and
>>> I want to
>>> create a 3D volume with this images.
>>>
>>> It would be de reverse operation of the class
>>> ExtractImageFilter.
>>>
>>> Does anybody knows how to do it?
>>>
>>> Thanks in advance,
>>> Luis
>>>
>>>
>>>
>>>
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========================================================
Bradley Lowekamp
Lockheed Martin Contractor for
Office of High Performance Computing and Communications
National Library of Medicine
blowekamp at mail.nih.gov
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