[Insight-developers] Orientation information being lost

[Luis Ibanez]

Hi Richard,


Image direction, along with origin, and spacing should be
copied automatically by "CopyInformation()" which in turn
is invoked by the call

     ProcessObject::GenerateOutputInformation().

In line 1108 of the file itkProcessObject.cxx


Are you overloading this method ?
(the method GenerateOutputInformation())

and if so:

A) Are you calling the method

        ProcessObject::GenerateOutputInformation().

     from your overloaded method ?

or


B)  Are you calling CopyInformation() yourself
     from your overloaded method ?



Please let us know,


      Thanks


            Luis


-------------------------------------------------------------------------------

On Tue, Mar 9, 2010 at 1:12 AM, Richard Beare <richard.beare at gmail.com> wrote:
> Hi,
> I'm using a seeed region growing filter (one of mine) to carry out a
> simple segmentation. The filter doesn't do anything unusual in terms
> of creating output images, simply using the AllocateOutputs() call.
> The input image and input seeds have the following orientation
> information reported by fslhd:
>
> qform_name     Unknown
> qform_code     0
> qto_xyz:1      0.027032  0.000000  0.000000  0.000000
> qto_xyz:2      0.000000  0.027032  0.000000  0.000000
> qto_xyz:3      0.000000  0.000000  0.027032  0.000000
> qto_xyz:4      0.000000  0.000000  0.000000  1.000000
> qform_xorient  Left-to-Right
> qform_yorient  Posterior-to-Anterior
> qform_zorient  Inferior-to-Superior
> sform_name     Unknown
> sform_code     0
> sto_xyz:1      0.000000  0.000000  0.000000  0.000000
> sto_xyz:2      0.000000  0.000000  0.000000  0.000000
> sto_xyz:3      0.000000  0.000000  0.000000  0.000000
> sto_xyz:4      0.000000  0.000000  0.000000  0.000000
> sform_xorient  Unknown
> sform_yorient  Unknown
> sform_zorient  Unknown
>
>
> My output has the following orientation, even if I do a
> CopyInformation call using the input image as the template:
>
> qform_name     Aligned Anat
> qform_code     2
> qto_xyz:1      -0.027032  0.000000  0.000000  -0.000000
> qto_xyz:2      0.000000  -0.027032  0.000000  -0.000000
> qto_xyz:3      0.000000  0.000000  0.027032  0.000000
> qto_xyz:4      0.000000  0.000000  0.000000  1.000000
> qform_xorient  Right-to-Left
> qform_yorient  Anterior-to-Posterior
> qform_zorient  Inferior-to-Superior
> sform_name     Scanner Anat
> sform_code     1
> sto_xyz:1      -0.027032  0.000000  0.000000  -0.000000
> sto_xyz:2      0.000000  -0.027032  0.000000  -0.000000
> sto_xyz:3      0.000000  0.000000  0.027032  0.000000
> sto_xyz:4      0.000000  0.000000  0.000000  1.000000
> sform_xorient  Right-to-Left
> sform_yorient  Anterior-to-Posterior
> sform_zorient  Inferior-to-Superior
> file_type      NIFTI-1+
> file_code      1
>
> Is this something to do with sform information not being set? Any
> suggestions as to the correct way to deal with this?
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