[ITK] [ITK-users] Geodesic level set error

[Sindhoor Bhat]

Thanks Nicolas.
Actually I've tried without ROI filter  too. There was an error.
But ll check again & if i succeed will post it here.

If anyone else has similar issue & had solved, pls let me know. 

Thank you.


On Tuesday, 17 June 2014 6:45 PM, Nicolas Gallego <nicgallego at gmail.com> wrote:
 


Hi Sindhoor,
Since you are changing the size of the images via the RegionOfInterestFilter, then  you should check that the images provided to your fast marching filter are on the same physical space.
this fragment of code taken form the Examples/Segmentation/FastMarchingImageFilter.cxx
works because the image region size is that of the BufferedRegion of the reader.
With the information you have provided that's what I can suggest to check, if anybody has particular experience with this FastMarchingImageFilter that should be taken into account it would be appreciated.



Nicolás Gallego-Ortiz
Université catholique de Louvain, Belgium



2014-06-17 14:07 GMT+02:00 Sindhoor Bhat <bhatsindhoor at ymail.com>:

Hi Nicolas,
>
>
>Thanks for reply. This is what I did . Added below code to all filters & got origin & spacing of image
>
>
>                       OutputImageType:: Pointer image2= sigmoidFilter->GetOutput();
>                               image2->Print( std::cout ). 
>
>
>But there is no problem with all the filters used. There is a problem when it comes to fast marching. 
> fastMarching->SetOutputSize( roi_filter->GetOutput()->GetBufferedRegion().GetSize() ); //took o/p from roi filter (after reading---ROI----gradient magnitude etc )
>
>
>
>* In itk manual I've one doubt (image attached). They say take buffer region from smoothing filter , but have taken o/p from reader. That is not clear. 
>
>
>Can you pls tell what is wrong?
>
>
>
>On Tuesday, 17 June 2014 2:26 PM, Nicolas Gallego <nicgallego at gmail.com> wrote:
> 
>
>
>Hi Sindhoor,
>
>It's hard to tell. Could you provide a simple code that reproduces your error?
>A priori I would say you could print the image information on each connection of your pipeline, pay special attention to filters that may change it, as the ROI filter...
>Refer also to the concepts of regions: there are
>LargestPossibleRegion
>BufferedRegion
>RequestedRegion
>
>LargestPossibleRegion refers to the whole dataset. Refer to section 13.1 of the software guide for more details.
>I hope that helps,
>
>
>
>Nicolás Gallego-Ortiz
>Université catholique de Louvain, Belgium
>
>
>
>2014-06-17 10:36 GMT+02:00 Sindhoor Bhat <bhatsindhoor at ymail.com>:
>
>Hi nicgallego,
>>Thanks for reply.
>>I've read that section. Here is some detail on steps i followed. This may help you to give some hints.
>>
>>
>>1.read dicom series
>>2.define region of interest (ROI filter)
>>3. compute gradient & speed image.
>>4.Set seed using fast marching filter.
>>5.Give this inital level set image---- to geodesic segmentation filter
>>
>>
>>  geodesicActiveContour->SetInput(  fastMarching->GetOutput() );
>>  geodesicActiveContour->SetFeatureImage( sigmoidFilter->GetOutput() );
>>
>>
>>  fastMarching->SetOutputSize(roi_filter->GetOutput()->GetBufferedRegion().GetSize() ); //roi=region of interest
>>
>>
>>
>> Even after reading from same dicom series, why is this error? it should have same origin / spacing right?
>> can you pls help me ?
>>  
>>
>>
>>
>>On Tuesday, 17 June 2014 12:59 PM, Nicolas Gallego <nicgallego at gmail.com> wrote:
>> 
>>
>>
>>Good morning Sindhoor,
>>
>>In general itk pipelines process images in the physical space, so that pixelwise operations are between samples on the same physical position.
>>Section 4.1.4 of the Software guide [1] and its correspondent example (Image4.cxx) may help you,
>>
>>[1] http://www.itk.org/ItkSoftwareGuide.pdf
>>
>>
>>
>>Nicolás Gallego-Ortiz
>>Université catholique de Louvain, Belgium
>>
>>
>>
>>2014-06-17 7:28 GMT+02:00 Sindhoor Bhat <bhatsindhoor at ymail.com>:
>>
>>Dear Matt,
>>>
>>>
>>>I've got error in Geodesic active contour level set segmentation :  saying
>>> itk::ERROR: GeodesicActiveContourLevelSetImageFilter(0000000004AC7160): Inputs do not occupy the same physical space! 
>>>
>>>
>>>I searched a lot on solving this error. but none have replied. Can you pls tell how to solve this error?
>>>(I'm trying to segment 3D dicom images)
>>>
>>>
>>>thank you.
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>>
>>
>>
>
>
>
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