[Insight-users] ITK 3.12 : Scheduled for Feb 28 2009

[Ivan Macia]

Hi Luis,

IMHO direction should be a 3x3 matrix, since a slice has an orientation in
3D space that for example is specified in the DICOM (DICOM also specifies
Image Position too). For example, we use a cache strategy that allows us to
load slices of a volume for visualization on demand. At the time of
reconstructing the volume, we use this 3D direction in order to generate the
volume (3D ITK image).

There are times that a DICOM Series mixes images with different orientation
where this information would be useful. For example, there are series that
consist of a reformatted volume, let's say in axial orientation, whose first
image is a coronal screenshot that represents the reconstructed area of the
reformatted volume that follows. It seems reasonable to me to keep this
information without having to recur to the DICOM metadata. The same argument
could be applied to the image position, which is also 3D.

But probably there are other considerations, such as the Analyze format you
mention and other requirement or implementation issues that I am not aware
of.

In any case, thanks in advance for looking into this.

Iván


2009/2/22 Luis Ibanez <luis.ibanez at kitware.com>

>
> Hi Ivan,
>
> Thanks for pointing this out,
> and thanks for sharing your images.
>
>
> As described in the bug report, the offending code is in the
> ImageFileReader.
>
> We are looking at options that would result in a reasonable
> behavior.
>
> The challenge is that:
>
>
>   a) When reading 3D Direction cosines into a 2D image,
>      we only keep a 2x2 matrix. This matrix doesn't really
>      map to 3D space
>
>   b) The current code manually modify the matrices to
>      satisfy the restrictions of the Analyze file format,
>      but it doesn't address all the cases
>
>   c) The naive solution of setting the directions to an
>      identiy will result in an orientation that is not
>      supported by Analyze.
>
>
> We are looking into this...
>
>
>   Thanks
>
>
>      Luis
>
>
> ------------------
> Ivan Macia wrote:
>
>> Hi Luis, all,
>>
>> I dont know if this could be an outstanding issue or we are doing
>> something wrong but for us it is. Since version ITK-3.10 and on, we are not
>> able to load ANY coronal or sagittal slice with a simple
>> itk::ImageFileReader for a 2D image. An exception is always thrown in
>> itk::ImageBase::ComputeIndexToPhysicalPointMatrices() complaining about the
>> direction matrix being singular. This prevents us to switch to ITK-3.10 or
>> future ITK-3.12 since our ITK-based software stopped working correctly.
>>
>> This was posted in the developers list some time ago but unfortunately got
>> no answer this time :(
>> See detailed description here.
>>
>> http://public.kitware.com/Bug/view.php?id=8470
>>
>> Can anyone please try to reproduce this error? You may used attached Dicom
>> files to this email, one is coronal and one is sagittal. I tried with
>> ImageReadWrite example in ITK-3.10.1. This works in ITK-3.8.0.
>> I have set ITK_USE_ORIENTED_IMAGE_DIRECTION ON in CMake, but I think this
>> should still work with this setting isn't it?
>>
>> Thanks in advance for your help
>>
>> Ivan
>>
>>
>>
>> 2009/2/20 Luis Ibanez <luis.ibanez at kitware.com <mailto:
>> luis.ibanez at kitware.com>>
>>
>>
>>    Just to let you know that the release of ITK 3.12
>>    is scheduled for Feb 28.
>>
>>    During the following week we will be cleaning up
>>    the Dashboard.
>>
>>    If you see any outstanding issue,
>>    please let us know,
>>
>>
>>     Thanks
>>
>>
>>      Luis
>>
>>
>>    _____________________________________
>>    Powered by www.kitware.com <http://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-users
>>
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20090222/59862d62/attachment.htm>