[ITK Community] Resampling and origin patient for DICOM files
Luis Ibanez
luis.ibanez at kitware.com
Mon Mar 17 13:59:18 EDT 2014
Guillaume,
Yes, using the GDCM classes in ITK, for processing all the DICOM series
(both for reading and writing) will be a good way of enforcing consistency
on the management of the coordinate systems.
Regards,
Luis
On Mon, Mar 17, 2014 at 11:59 AM, Guillaume Lemaître <g.lemaitre58 at gmail.com
> wrote:
> Thanks Luis,
>
> I didn't think yet about suggestion A) and it solves already one of the
> issue that I observed.
>
> Regarding the other orientation problem, I think I see the problem more
> clearly. The relevant thing that I didn't consider at first is:
>
> 1. Extract Image<http://www.itk.org/Doxygen/html/classitk_1_1Image.html> Orientation
> & Image <http://www.itk.org/Doxygen/html/classitk_1_1Image.html> Position
> from DICOM images, and then calculate the ordering based on the 3D
> coordinate of the slice
>
> And I saw that the last image in the serie becomes the origin so it should
> be something related with the acquisition performed in the "reverse way"
> when considering the 3D coordinates.
> Probably, I could start by receiving all the series using GDCM, which
> would avoid any trouble with the header after.
>
> Thanks,
>
> Best regards,
>
>
> On 17 March 2014 16:36, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
>> Hi Guillaume,
>>
>>
>> Thanks for the detailed description of what you are trying to do.
>>
>>
>> A) When resampling an image mask, please make sure to use the
>>
>> NearestNeighbor interpolator,
>>
>> so that the values of the mask are not blended in the borders.
>>
>>
>> B) Your expectation on the behavior of the origin is correct.
>>
>> You are correctly feeding to the ResampleImageFilter the
>> parameters of the target image:
>>
>> Origin
>> Spacing
>> Direction
>> Size
>>
>> C) Make sure that the "targetVolume" source of the image
>> has been updated BEFORE you take the values from
>> it output. That is, if the targetVolume class is a file reader,
>> then you may want to do something like:
>>
>> targetVolume->Update();
>> const TargetImageType * targetImage = targetVolume->GetOutput();
>>
>> resampler->SetOutputOrigin( targetImage->GetOrigin() );
>> resampler->SetOutputSpacing( targetImage->GetSpacing() );
>> resampler->SetOutputDirection(
>> targetImage->GetOutput()->GetDirection() );
>> resampler->SetSize(
>> targetImage->GetLargestPossibleRegion().GetSize() );
>>
>> resampler->Update();
>>
>>
>> D) At the moment of registering, what really matters is the Origin value
>> inside ITK, regardless of whether it matches the one in the DICOM
>> tags.
>>
>> E) At the moment of saving the resampled mask into a DICOM file(s),
>> you can then cross check whether the origin tags in the resampled
>> mask DICOM file, matches the ones from the targetVolume DICOM files.
>>
>> That is, give ITK and GDCM the opportunity to the the proper magic
>> in the process of reading and writing the image.
>>
>>
>> Please let us know if you run into any questions, as you do this.
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>>
>>
>> On Mon, Mar 17, 2014 at 7:38 AM, Guillaume Lemaître <
>> g.lemaitre58 at gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> I am currently working on the following task. I got two DICOM series
>>> from different modality with different spacing, and origin. A third DICOM
>>> serie correspond to binary segmentation of one the previous serie. I would
>>> like to "project" this segmentation into the other serie. I think that the
>>> resampling filter should make this work quite well. It should look
>>> something like that:
>>>
>>> ResampleFilterType::Pointer resampler = ResampleFilterType::New();
>>> resampler->SetInput( maskVolume->GetOutput() );
>>> resampler->SetTransform( transform );
>>> resampler->SetInterpolator( interpolator );
>>> resampler->SetOutputOrigin( targetVolume->GetOutput()->GetOrigin() );
>>> resampler->SetOutputSpacing( targetVolume->GetOutput()->GetSpacing() );
>>> resampler->SetOutputDirection(
>>> targetVolume->GetOutput()->GetDirection() );
>>> resampler->SetSize(
>>> targetVolume->GetOutput()->GetLargestPossibleRegion().GetSize() );
>>> resampler->Update();
>>>
>>> However, I got trapped with what seems to be a problem of origin. I
>>> search around and different discussions and got quite confused. From what I
>>> found is the following:
>>> Using gdcminfo to read the origin of targetVolume will give me the same
>>> information than the tag (0020,0032) of the DICOM header. However, it will
>>> be different from targetVolume->GetOuput()->GetOrigin() which imply a shift
>>> when saving my data later.
>>>
>>> What should the proper way to do such task?
>>>
>>> Thanks in advance,
>>>
>>> Best regards,
>>> --
>>>
>>>
>>>
>>>
>>> *LEMAÎTRE Guillaume PhD CandiateMSc Erasmus Mundus ViBOT
>>> (Vision-roBOTic)MSc Business Innovation and Technology Management (in
>>> progress) *
>>> g.lemaitre58 at gmail.com
>>>
>>> *ViCOROB - Computer Vision and Robotic Team*
>>> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona
>>> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59
>>> http://vicorob.udg.es/
>>>
>>> *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la
>>> Fonderie, 71200 Le Creusot
>>> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97
>>> http://le2i.cnrs.fr
>>>
>>> https://sites.google.com/site/glemaitre58/
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>>>
>>> _______________________________________________
>>> Community mailing list
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>>>
>>>
>>
>
>
> --
>
>
>
>
> *LEMAÎTRE Guillaume PhD CandiateMSc Erasmus Mundus ViBOT
> (Vision-roBOTic)MSc Business Innovation and Technology Management (in
> progress) *
> g.lemaitre58 at gmail.com
>
> *ViCOROB - Computer Vision and Robotic Team*
> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona
> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59
> http://vicorob.udg.es/
>
> *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la
> Fonderie, 71200 Le Creusot
> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97
> http://le2i.cnrs.fr
>
> https://sites.google.com/site/glemaitre58/
> Vice - Chairman of A.S.C. Fours UFOLEP
> Chairman of A.S.C. Fours FFC
> Webmaster of http://ascfours.free.fr
>
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