[Insight-developers] Re: strategies for orientation of mouse MRI

[Richard Beare]

Hi everyone,

the fsl problem was related to data types - fsl doesn't like unsigned short.

On 9/6/07, Richard Beare <richard.beare at gmail.com> wrote:
> Hi everyone,
>
> I'm reorienting mouse MRI scans using the OrientImageFilter. I seem to
> be able to get this working sensibly by specifying the input
> orientation and desired output orientation. My output nifti images are
> viewable with ImageViewer, but seem to crash fslview. I'm wondering if
> I'm forgetting something that results in invalid nifti files. fslview
> is able to load the original images which were converted from Bruker
> format using my preliminary ITK BrukerIO module.
>
> The nifti information from the original is
>
> qform_code           252      1    1
>   sform_code           254      1    1
>   quatern_b            256      1    0.0
>   quatern_c            260      1    0.0
>   quatern_d            264      1    1.0
>   qoffset_x            268      1    -0.0
>   qoffset_y            272      1    -0.0
>   qoffset_z            276      1    0.0
>   srow_x               280      4    -0.03 0.0 0.0 -0.0
>   srow_y               296      4    0.0 -0.017578 0.0 -0.0
>   srow_z               312      4    0.0 0.0 0.03 0.0
>   intent_name          328     16
>
> After manipulation via:
>
>   orienter->SetGivenCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_IAL);
>   orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RIA);
> qform_code           252      1    1
>   sform_code           254      1    1
>   quatern_b            256      1    -0.5
>   quatern_c            260      1    0.5
>   quatern_d            264      1    0.5
>   qoffset_x            268      1    11.97
>   qoffset_y            272      1    -0.0
>   qoffset_z            276      1    0.0
>   srow_x               280      4    -0.0 -0.03 0.0 11.97
>   srow_y               296      4    -0.0 0.0 -0.017578 -0.0
>   srow_z               312      4    -0.03 0.0 0.0 0.0
>   intent_name          328     16
>
>
> Am I doing anything obviously wrong?
>