[Insight-users] Interpolation Volume
Luis Ibanez
luis.ibanez at kitware.com
Fri Dec 11 20:46:55 EST 2009
Hi Gupt,
You mentioned that you *resized* the PNG slices.
Did you resized them to be all of the *exact same* size ?
The series reader requires that all the slices have the
exact same number of pixels...
Please try calling
try
{
reader->Update();
}
catch( itk::ExceptionObject & err )
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
before you call Update() in the writer.
and see if you get any error.
We need to discriminate between errors
from the process of reading the series
and errors from the process of writing
the image out.
Please let us know what you find,
Thanks
Luis
--------------------------------------------------------------------------
On Wed, Dec 9, 2009 at 11:14 AM, Gupt <adityargupta at gmail.com> wrote:
>
> Hello Luis,
>
> I'm using the ImageSeriesReadWrite example from ITK User guide. I'm reading
> a set of 2d png images and writing to a 3d file. Irene280052.png to
> Irene280061.png - grayscale images of size 131 X141. With the program below,
> at the command prompt I call the program with parameters >>ImageReadWrite 52
> 61 out1.mhd.
>
> Program:
>
> #include "itkImage.h"
> #include "itkImageSeriesReader.h"
> #include "itkImageFileWriter.h"
> #include "itkNumericSeriesFileNames.h"
> #include "itkPNGImageIO.h"
>
> int main( int argc, char ** argv )
> {
> // Verify the number of parameters in the command line
> if( argc < 4 )
> {
> std::cerr << "Usage: " << std::endl;
> std::cerr << argv[0] << " firstSliceValue lastSliceValue
> outputImageFile " << std::endl;
> return EXIT_FAILURE;
> }
>
> typedef unsigned char PixelType;
> const unsigned int Dimension = 3;
>
> typedef itk::Image< PixelType, Dimension > ImageType;
> typedef itk::ImageSeriesReader< ImageType > ReaderType;
> typedef itk::ImageFileWriter< ImageType > WriterType;
>
> ReaderType::Pointer reader = ReaderType::New();
> WriterType::Pointer writer = WriterType::New();
>
> const unsigned int first = atoi( argv[1] );
> const unsigned int last = atoi( argv[2] );
>
> const char * outputFilename = argv[3];
>
> typedef itk::NumericSeriesFileNames NameGeneratorType;
>
> NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
>
> nameGenerator->SetSeriesFormat( "Irene2800%02d.png" );
>
> nameGenerator->SetStartIndex( first );
> nameGenerator->SetEndIndex( last );
> nameGenerator->SetIncrementIndex( 1 );
>
> reader->SetImageIO( itk::PNGImageIO::New() );
> reader->SetFileNames( nameGenerator->GetFileNames() );
>
> writer->SetFileName( outputFilename );
> writer->SetInput( reader->GetOutput() );
> try
> {
> writer->UpdateLargestPossibleRegion();
> writer->Update();
> }
> catch( itk::ExceptionObject & err )
> {
> std::cerr << "ExceptionObject caught !" << std::endl;
> std::cerr << err << std::endl;
> return EXIT_FAILURE;
> }
> return EXIT_SUCCESS;
> }
>
>
> The images are the slices of the heart which I converted from DICOM to png
> and did some image processing operations - improving resolution, resizing.
> Is the problem related to the images I'm using?
>
> Thanks.
>
> Regards,
> Gupt
>
>
>
>
> Luis Ibanez wrote:
>>
>> Hi Gupt,
>>
>> We are talking about two different problems here.
>>
>> In your previous email, we dealt with a Reading problem
>> that happens when a reader is reused for loading images
>> of different sizes.
>>
>> That seems to have been fixed with the use of method
>>
>> reader->UpdateLargestPossibleRegion().
>>
>> ...
>>
>> Now, we seem to be dealing with a problem in the output
>> of your program.
>>
>> Please tell us what happens in the middle (between the
>> reader and the writer).
>>
>> Are you simply reading a series of 2D images, and then
>> writing them out right away ?
>>
>>
>> If your program is a single file (source code), and if it is not
>> too long (less than 30Kb), it will be very helpful if you can
>> post your source code to the mailing list.
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> ------------------------------
>> On Tue, Dec 8, 2009 at 4:17 PM, Gupt <adityargupta at gmail.com> wrote:
>>>
>>> Hello Luis,
>>>
>>> Using UpdateLargestPossibleRegion() didn't give me the error for one set
>>> of
>>> slices but the mhd (raw and hdr) file created had errors. When I try to
>>> open
>>> the volume using MRIcro, I get the error -
>>>
>>> Unknown image format, and file size smaller than described in 'Header
>>> Information' panel.
>>>
>>> I also tried using ITK SNAP but am unable to open the file.
>>>
>>> When I re-run the program for a different set of slices, I get the error
>>> described in my last post - "Largest possible region does not fully
>>> contain
>>> requested paste IO regionPaste IO region:..."
>>>
>>> Thank you for your help.
>>>
>>> Regards,
>>> Gupt
>>>
>>> Luis Ibanez wrote:
>>>>
>>>> Hi Gupt,
>>>>
>>>> This error is usually produced when you attempt to "reuse" a
>>>> reader to load two images of different size, one after another.
>>>>
>>>> For example:
>>>>
>>>> reader->SetFileName("myImage1.mhd");
>>>> reader->Update();
>>>>
>>>> reader->SetFileName("myImage2.mhd");
>>>> reader->Update();
>>>>
>>>>
>>>> The simple solution is to call "UpdateLargestPossibleRegion()"
>>>> instead of calling the typical "Update()" method.
>>>>
>>>> So your code your look more like:
>>>>
>>>>
>>>> reader->SetFileName("myImage1.mhd");
>>>> reader->UpdateLargestPossibleRegion();
>>>>
>>>> reader->SetFileName("myImage2.mhd");
>>>> reader->UpdateLargestPossibleRegion();
>>>>
>>>>
>>>> Please let us know if that helps,
>>>>
>>>>
>>>> Thanks
>>>>
>>>>
>>>> Luis
>>>>
>>>>
>>>> --------------------------------------------------------------------------------------------------------
>>>> On Mon, Dec 7, 2009 at 5:11 PM, Gupt <adityargupta at gmail.com> wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> I'm working with ImageSeriesReadWrite.cxx example from ITK user guide.
>>>>> I'm
>>>>> trying to build the 3d volume from a set of 2d mri images -
>>>>> file280054.jpg
>>>>> to file280062.jpg. But I'm receiving the following error:
>>>>>
>>>>> ExceptionObject Caught!
>>>>>
>>>>> itk:ExceptionObject <0134F560>
>>>>> itk::Location: "void __thiscall itk::ImageFileWriter<class
>>>>> itk::Image<unsigned
>>>>> char,3> >::Write(void)"
>>>>> File: c:\itk\insight_toolkit\code\io\itkImageFileWriter.txx
>>>>> Line: 271
>>>>> Description: itk::ERROR: ImageFileWriter(01934508): Largest possible
>>>>> region
>>>>> does not fully contain requested paste IO regionPaste IO region:
>>>>> ImageIORegion (0134F998)
>>>>> Dimension: 3
>>>>> Index: 0 0 0
>>>>> Size: 0 0 0
>>>>> Largest possible region: ImageRegion (0134FA4C)
>>>>> Dimension: 3
>>>>> Index: [0, 0, 0]
>>>>> Size: [0, 0, 0]
>>>>>
>>>>> Thanks for your help.
>>>>>
>>>>> Gupt
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Luis Ibanez wrote:
>>>>>>
>>>>>> Hi Gupt,
>>>>>>
>>>>>> We no longer make any difference between a sequence of 2D slices
>>>>>> and a 3D volume... unless.... they are not aligned, or... the spacing
>>>>>> in
>>>>>> the inter-slice direction is more than 5 times the intra-slice
>>>>>> spacing.
>>>>>>
>>>>>>
>>>>>> If you have segmentations for all the 2D slices, you can simply load
>>>>>> them
>>>>>> all into a single 3D image using an ImageSeriesReader, and then you
>>>>>> can process it as a 3D volume. More specifically, you can proceed to
>>>>>> compute its volume by using the LabelStatisticsImageFilter.
>>>>>>
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>>
>>>>>> Luis
>>>>>>
>>>>>>
>>>>>> --------------------------------
>>>>>> On Mon, Dec 7, 2009 at 12:10 PM, Aditya Gupta <adityargupta at gmail.com>
>>>>>> wrote:
>>>>>>> Hello Luis,
>>>>>>>
>>>>>>> Thanks for the reply. In continuation to my previous question... So
>>>>>>> using
>>>>>>> the stack of 2d MRI slices, I've a certain segmentation on each of
>>>>>>> the
>>>>>>> slices and using the segmented output I've built a surface model and
>>>>>>> now
>>>>>>> I've incorporated the intensities of the slices in the surface model.
>>>>>>> Now,
>>>>>>> I'm interested to find the volume of the segmented region. So, using
>>>>>>> the
>>>>>>> segmented outputs from the various slices, I want to reconstruct a
>>>>>>> volume,
>>>>>>> compute and finally visualize the volume. Can you give me a start on
>>>>>>> how
>>>>>>> I
>>>>>>> can proceed? Is it possible to build a 3d volume (not surface model)
>>>>>>> from
>>>>>>> a
>>>>>>> stack of 2d slices (only one axial view not 3 views)? Are there any
>>>>>>> standard
>>>>>>> algorithms being used for construction of 3d volumes from 2d slices?
>>>>>>>
>>>>>>> Appreciate your help in this matter.
>>>>>>>
>>>>>>> Regards,
>>>>>>> Gupt
>>>>>>>
>>>>>>> On Wed, Dec 2, 2009 at 7:07 PM, Luis Ibanez <luis.ibanez at kitware.com>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Hi Gupt,
>>>>>>>>
>>>>>>>>
>>>>>>>> Yes, just do the following:
>>>>>>>>
>>>>>>>>
>>>>>>>> A) Load the 2D slices into a single 3D image using the
>>>>>>>> itk::ImageSeriesReader,
>>>>>>>>
>>>>>>>>
>>>>>>>> B) Connect the image an ImageInterpolator
>>>>>>>> The typical choice is the itkLinearImageInterpolateFunction
>>>>>>>> class,
>>>>>>>> (but you can also use NearestNeighbors, BSpline and
>>>>>>>> WindowedSinc, it is a trade-off between computation time and
>>>>>>>> interpolation precision)
>>>>>>>>
>>>>>>>>
>>>>>>>> C) Take all the points from your surface model and for every
>>>>>>>> point call the method:
>>>>>>>>
>>>>>>>> PixelType pixelValue = Interpolator->Evaluate( point )
>>>>>>>>
>>>>>>>> and then assign that pixel value to the corresponding point
>>>>>>>> in the surface model.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Please let us know if you run into any problem.
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>>
>>>>>>>> Luis
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------
>>>>>>>> On Wed, Dec 2, 2009 at 2:35 PM, Gupt <adityargupta at gmail.com> wrote:
>>>>>>>> >
>>>>>>>> > I've a stack of 2d cardiac mri images in single view. I've written
>>>>>>>> the
>>>>>>>> > code
>>>>>>>> > to do a surface reconstruction of the left ventricle wall of the
>>>>>>>> heart
>>>>>>>> > (looks like a hollow cylinder). Is there a method/ function to
>>>>>>>> > incorporate
>>>>>>>> > the intensity information (in the 2d slices) in to the model, like
>>>>>>>> some
>>>>>>>> > kind
>>>>>>>> > of interpolation to obtain intensity between the slices? Thanks
>>>>>>>> for
>>>>>>>> the
>>>>>>>> > help.
>>>>>>>> > --
>>>>>>>> > View this message in context:
>>>>>>>> >
>>>>>>>> http://old.nabble.com/Interpolation-Volume-tp26614974p26614974.html
>>>>>>>> > Sent from the ITK - Users mailing list archive at Nabble.com.
>>>>>>>> >
>>>>>>>> > _____________________________________
>>>>>>>> > Powered by www.kitware.com
>>>>>>>> >
>>>>>>>> > Visit other Kitware open-source projects at
>>>>>>>> > http://www.kitware.com/opensource/opensource.html
>>>>>>>> >
>>>>>>>> > Kitware offers ITK Training Courses, for more information visit:
>>>>>>>> > http://www.kitware.com/products/protraining.html
>>>>>>>> >
>>>>>>>> > Please keep messages on-topic and check the ITK FAQ at:
>>>>>>>> > http://www.itk.org/Wiki/ITK_FAQ
>>>>>>>> >
>>>>>>>> > Follow this link to subscribe/unsubscribe:
>>>>>>>> > http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Regards,
>>>>>>> Aditya Gupta, Ph.D.
>>>>>>> Post Doc Researcher
>>>>>>> UCF Computer Vision Lab
>>>>>>> Orlando, FL
>>>>>>> O: (407) 882 0130
>>>>>>> M: (407) 451 7735
>>>>>>>
>>>>>> _____________________________________
>>>>>> Powered by www.kitware.com
>>>>>>
>>>>>> Visit other Kitware open-source projects at
>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>
>>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>>> http://www.kitware.com/products/protraining.html
>>>>>>
>>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>>
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>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> View this message in context:
>>>>> http://old.nabble.com/Interpolation-Volume-tp26614974p26685129.html
>>>>> Sent from the ITK - Users mailing list archive at Nabble.com.
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.html
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.html
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
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>>>> http://www.itk.org/mailman/listinfo/insight-users
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>>>>
>>>
>>> --
>>> View this message in context:
>>> http://old.nabble.com/Interpolation-Volume-tp26614974p26700914.html
>>> Sent from the ITK - Users mailing list archive at Nabble.com.
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.html
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
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>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
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>>
>
> --
> View this message in context: http://old.nabble.com/Interpolation-Volume-tp26614974p26712924.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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