[Insight-developers] world coordinates and slice images - nifti problem?

[Richard Beare]

Hi,

I'll have to wait until next week to post images (at work).

The situation is this. I have two images, each of which is a time
series with a single physical slice.

I convert load each dicom from the timeseries into a itk::Image<short,
3> and save as a nifti file. So I certainly hoped that this is a 3d
nifti file with one slice. Tools like fslinfo certainly report a z
dimension of 1 and 3 dimensions.

I was certainly aiming to get a 3d image on disk with one slice. I
hope that is what I achieved.

I'm after full 3D information so I can display a collection of slices
like this in their correct relative orientation.

Should this be feasible?

On Fri, Feb 27, 2009 at 11:28 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
> Hi Richard,
>
>
> I'm having trouble understanding your description of the problem.
>
>
> You said:
>> My problem is that even though I declare the image as 3D, it only has
>> 1 slice, and the PhysicalPoints produced by the transformation all
>> have a z value of 0. If I concatenate two slices together the results
>> are as I expect. On the surface it looks like it might be a nifti
>> loading issue
>
>
>
> Your message is not telling us what the actual image in disk is.
>
> For example:
>
>   a) Is the image on file a 3D image ?
>   b) If so, does it really have more than 1 slice ?
>
> or
>
>   c) Are you tring to read a 2D nifti image file
>      into an itk::Image< Pixel, 3 > type ?
>
>
> If the situation is (c), then the behavior looks quite normal.
>
> but
>
> if the situation is that your have a 3D image with more than
> one slice on file, and when you read it into an ITK 3D image,
> you only get one slice, then that's clearly a bug.
>
>
> Could you please clarify ?
>
> and...
>
> Please post to the list:
>
>  A) The offending Nifti image, and
>  B) The (minima) source code that illustrates the problem
>
>
> Thanks,
>
>
>    Luis
>
>
> ---------------------
> Richard Beare wrote:
>>
>> Hi,
>> I'm not sure if this counts as a bug, and I haven't tracked down the
>> root of the issue yet, but thought I'd flag it immediately.
>>
>> This relates to the same data as my past few posts - single slice MR
>> time series which I'm trying to do preliminary visualization on.
>>
>> One of my approaches uses the world coordinates as reported by the
>> TransformIndexToPhysicalPoint method of OrientedImage.
>>
>> My problem is that even though I declare the image as 3D, it only has
>> 1 slice, and the PhysicalPoints produced by the transformation all
>> have a z value of 0. If I concatenate two slices together the results
>> are as I expect. On the surface it looks like it might be a nifti
>> loading issue
>>
>> The differences in image information are (interesting one last):
>>
>> single slice
>>
>>  RequestedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [256, 256, 1]
>>  Spacing: [1.25, 1.25, 1]
>>  Origin: [-160.625, -157.719, 0]
>>  Direction:
>> 1 0 0
>> 0 1 0
>> 0 0 1
>>
>>  IndexToPointMatrix:
>>  1.25 0 0
>> 0 1.25 0
>> 0 0 1
>>
>>  PointToIndexMatrix:
>>  0.8 0 0
>> 0 0.8 0
>> 0 0 1
>>
>> slice pair
>>
>>  RequestedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [256, 256, 2]
>>  Spacing: [1.25, 1.25, 5]
>>  Origin: [-160.625, -157.719, 9.70944]
>>  Direction:
>> 1 0 0
>> 0 1 0
>> 0 0 1
>>
>>  IndexToPointMatrix:
>>  1.25 0 0
>> 0 1.25 0
>> 0 0 5
>>
>>  PointToIndexMatrix:
>>  0.8 0 0
>> 0 0.8 0
>> 0 0 0.2
>>
>>
>> Orthogonal slice
>> ---------------------
>>
>>  RequestedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [192, 256, 1]
>>  Spacing: [1.25, 1.25, 1]
>>  Origin: [-29.0319, -91.3025, 0]
>>  Direction:
>> 0.479759 0.985709 0
>> 0.8774 -0.168457 0
>> 0 0 1
>>
>>  IndexToPointMatrix:
>>  0.599698 1.23214 0
>> 1.09675 -0.210571 0
>> 0 0 1
>>
>>  PointToIndexMatrix:
>>  0.142507 0.833862 0
>> 0.742239 -0.405853 0
>> 0 0 1
>>
>> Orthogonal slice pair
>> --------------------------
>>  RequestedRegion:
>>    Dimension: 3
>>    Index: [0, 0, 0]
>>    Size: [192, 256, 2]
>>  Spacing: [1.25, 1.25, 4]
>>  Origin: [-29.0319, -91.3025, 135.198]
>>  Direction:
>> 0.47975 0.0179872 -0.877221
>> 0.877385 -0.00307401 0.479777
>> 0.00593328 -0.999833 -0.0172565
>>
>>  IndexToPointMatrix:
>>  0.599688 0.0224841 -3.50888
>> 1.09673 -0.00384251 1.91911
>> 0.0074166 -1.24979 -0.069026
>>
>>  PointToIndexMatrix:
>>  0.3838 0.701908 0.00474662
>> 0.0143898 -0.00245921 -0.799867
>> -0.219305 0.119944 -0.00431412
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.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-developers
>>
>