[Insight-users] Wrong origin when reading a nifti image saved with MIPAV

[Elena Faggiano]

Hi,

I've found that if i load a dicom image with MIPAV (last version) the
coordinate system (origin etc.) is the same as ITK, and this is the true
coordinate system.
If I decide to save with MIPAV the DICOM volume in a nifti format the
coordinate system changes!! So the problem is clearly a MIPAV's problem...

Now, what I do is open with MIPAV the DICOM volume make preprocessing on
DICOM volume and than save it in DICOM format too (in order to mantain the
correct origin and orientation).

anyways what I want to do as preprocessing is pad or cut the image or put
some markers on it.

Thanks

Elena Faggiano

2008/10/16 Luis Ibanez <luis.ibanez at kitware.com>

>
> Hi Elena,
>
> This looks like a problem in MIPAV, not really an ITK problem.
>
> If you are looking for applications for preprocessing images
> you may want to look at:
>
>
>    Slicer:   http://www.slicer.org/
>    SNAP:     http://www.itksnap.org/
>
>
> That are both build based on ITK and VTK.
>
>
> What kind of pre-processing do you need to apply to these images ?
>
>
>   Thanks
>
>
>      Luis
>
>
> -----------------------
> Elena Faggiano wrote:
>
>> Hi,
>>
>> I have a CT image (series of images) in DICOM format and I read it with
>> DicomSeriesImageWrite, and I write a nifti file (.nii).
>> Then I read the nifti image with an ImageFileReader and if I ask the
>> information about the DICOM image and the nifti image they are equal:
>>
>> for the DICOM image:
>> /OrientedImage (0x8f92fd0)
>>  RTTI typeinfo:   itk::OrientedImage<short, 3u>
>>  Reference Count: 1
>>  Modified Time: 2592
>>  Debug: Off
>>  Observers:
>>    none
>>  Source: (0x8f908e8)
>>  Source output index: 0
>>  Release Data: Off
>>  Data Released: False
>>  Global Release Data: Off
>>  PipelineMTime: 18
>>  UpdateMTime: 2593
>>  LargestPossibleRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [512, 512, 101]
>>  BufferedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [512, 512, 101]
>>  RequestedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [512, 512, 101]
>>  Spacing: [1.36719, 1.36719, 2.5]
>>  Origin: [-350, -350, -402]
>>  Direction:
>> 1 0 0
>> 0 1 0
>> 0 0 1
>>
>>  PixelContainer:
>>    ImportImageContainer (0x8f93188)
>>      RTTI typeinfo:   itk::ImportImageContainer<//unsigned long, short>
>>      Reference Count: 1
>>      Modified Time: 66
>>      Debug: Off
>>      Observers:
>>        none
>>      Pointer: 0xb4d31008
>>      Container manages memory: true
>>      Size: 26476544
>>      Capacity: 26476544/
>>
>> for the NIFTI image:
>>  /RTTI typeinfo:   itk::OrientedImage<short, 3u>
>>  Reference Count: 1
>>  Modified Time: 119
>>  Debug: Off
>>  Observers:
>>    none
>>  Source: (0xa1788e8)
>>  Source output index: 0
>>  Release Data: Off
>>  Data Released: False
>>  Global Release Data: Off
>>  PipelineMTime: 12
>>  UpdateMTime: 120
>>  LargestPossibleRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [512, 512, 101]
>>  BufferedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [512, 512, 101]
>>  RequestedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [512, 512, 101]
>>  Spacing: [1.36719, 1.36719, 2.5]
>>  Origin: [-350, -350, -402]
>>  Direction:
>> 1 0 0
>> 0 1 0
>> 0 0 1
>>
>>  PixelContainer:
>>    ImportImageContainer (0xa17b198)
>>      RTTI typeinfo:   itk::ImportImageContainer<//unsigned long, short>
>>      Reference Count: 1
>>      Modified Time: 117
>>      Debug: Off
>>      Observers:
>>        none
>>      Pointer: 0xb4d22008
>>      Container manages memory: true
>>      Size: 26476544
>>      Capacity: 26476544/
>>
>>
>> Then I open the nifti image with MIPAV image viewer (
>> http://mipav.cit.nih.gov/download.php) and if I re-save it using MIPAV I
>> get incorrect origin:
>>
>> /OrientedImage (0x99ddfe0)
>>  RTTI typeinfo:   itk::OrientedImage<short, 3u>
>>  Reference Count: 1
>>  Modified Time: 119
>>  Debug: Off
>>  Observers:
>>    none
>>  Source: (0x99db8e8)
>>  Source output index: 0
>>  Release Data: Off
>>  Data Released: False
>>  Global Release Data: Off
>>  PipelineMTime: 12
>>  UpdateMTime: 120
>>  LargestPossibleRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [512, 512, 101]
>>  BufferedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [512, 512, 101]
>>  RequestedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [512, 512, 101]
>>  Spacing: [1.36719, 1.36719, 2.5]
>>  Origin: [-350, 350, -402]
>>  Direction:
>> 1 0 0
>> 0 1 0
>> 0 0 1
>>
>>  PixelContainer:
>>    ImportImageContainer (0x99de198)
>>      RTTI typeinfo:   itk::ImportImageContainer<//unsigned long, short>
>>      Reference Count: 1
>>      Modified Time: 117
>>      Debug: Off
>>      Observers:
>>        none
>>      Pointer: 0xb4cbf008
>>      Container manages memory: true
>>      Size: 26476544
>>      Capacity: 26476544/
>>
>>
>> I wonder that ti is a MIPAV problem but I'm not sure! I can't understand
>> why MIPAV changes the origin...Anyone knows this problem?
>>
>> And if the problem is MIPAV I can use something else to do some
>> pre-elaboration on the images and than work with itk?
>>
>> Thanks for any hints.
>> Elena Faggiano
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>>
>
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