[Insight-users] Transforming image to world coordinates with negative z axis

[Luis Ibanez]

Hi John,

Thanks a lot for posting the output of the Print() method.

It seems that the image is not being read as the last slice
begin located at:

                 Z = -359.750

Instead it is located at:


       Z = -35.685 + 2.5 * 107 =  +231.81

and... even if the spacing was negative,
it could have only got to:

       Z = -35.685 - 2.5 * 107 =  -303.18



This raises suspicion about what you call the


            "last DICOM slice..."


Are you sure that it belongs to the same Series
as the first slice ?


Also,
If you visualize the image that you can read with ITK,
does it look ok ?


BTW: As DICOM readers/viewers you may want to try:


     A) Slicer
        http://www.slicer.org

     B) VV
        http://www.midasjournal.org/browse/publication/288



Please let us know what you find.


     Thanks


        Luis


-------------------
John Drescher wrote:
>>You are right, this looks strange.
>>
>>
>>Please do the following:
>>
>>Just after you load your DICOM image into an ITK image,
>>call the Print() method in the resulting image, and post
>>the outcome to the mailing list.
>>
>>Your code should look something like
>>
>> imageSeriesReader->Update();
>>
>> imageSeriesReader->GetOutput()->Print( std::cout );
>>
>>
>>The output of the Print() method will help us to locate
>>the source of the problem.
>>
>>
> 
> 
> OrientedImage (01D5C650)
>   RTTI typeinfo:   class itk::OrientedImage<short,3>
>   Reference Count: 1
>   Modified Time: 2757
>   Debug: Off
>   Observers:
>     none
>   Source: (01D5C508)
>   Source output index: 0
>   Release Data: Off
>   Data Released: False
>   Global Release Data: Off
>   PipelineMTime: 30
>   UpdateMTime: 2758
>   LargestPossibleRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [512, 512, 107]
>   BufferedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [512, 512, 107]
>   RequestedRegion:
>     Dimension: 3
>     Index: [0, 0, 0]
>     Size: [512, 512, 107]
>   Spacing: [0.626953, 0.626953, 2.5]
>   Origin: [-174.6, -160.5, -35.685]
>   Direction:
> 1 0 0
> 0 1 0
> 0 0 1
> 
>   IndexToPointMatrix:
>   0.626953 0 0
> 0 0.626953 0
> 0 0 2.5
> 
>   PointToIndexMatrix:
>   1.59502 0 0
> 0 1.59502 0
> 0 0 0.4
> 
>   PixelContainer:
>     ImportImageContainer (01D5C8A0)
>       RTTI typeinfo:   class itk::ImportImageContainer<unsigned long,short>
>       Reference Count: 1
>       Modified Time: 81
>       Debug: Off
>       Observers:
>         none
>       Pointer: 03410040
>       Container manages memory: true
>       Size: 28049408
>       Capacity: 28049408
> 
> 
>>----
>>
>>
>>BTW: Why do you say that the direction cosines
>>
>>
>>>1 0 0
>>>0 1 0
>>>0 0 1
>>
>>look wrong to you ?
>>
> 
> I thought it should be
> 
> 1 0 0
> 0 1 0
> 0 0 -1
> 
> so that the z axis coordinate conversion would be handled correctly.
> 
> 
>>Given that the direction cosines in the DICOM header
>>are
>>
>>
>>>1.000000\0.000000\0.000000\0.000000\1.000000\0.000000
>>
>>It seems normal to have the Direction matrix to be an
>>identity matrix.
>>
> 
> Looks like I have to do some reading.
> 
> Thanks for your help,
> John
>