[Insight-users] Interpolation Volume
Luis Ibanez
luis.ibanez at kitware.com
Tue Dec 8 08:02:41 EST 2009
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
>>>> >
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>>>> > 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
>>
>> Follow this link to subscribe/unsubscribe:
>> 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:
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