[Insight-developers] Orientation information being lost

[Richard Beare]

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?