Thank you very much for your reply!
I'm embarrassed to say that I'm still confused about the issue.
I've checked the q/sform. How can I know whether the left/right issue is set correctly on the basis of the q/s form?
For instance, for one raw nifti image (coming from Lab2) converted from the dicoms and reoriented with fslreorient2std, the qform (code: 1, Scanner Anat) is:
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.000000 0.000000 -0.000000 87.500000
qto_xyz:2 0.000000 1.000000 -0.000000 -85.867477
qto_xyz:3 0.000000 0.000000 1.000000 -134.951813
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
Where should I go from that? When I travel from the i voxel coordinate from 0 to 175, the x coordinate decreases accordingly (going from 87.5 which by convention corresponds to the right, to -87.5 which by convention corresponds to the left) in a way that corresponds to the Right-to-Left orientation written in the qform. The fslorient says it's radiological.
Another image that comes from Lab1 has this s/qform once reoriented with fslreorient2std:
sform_name Scanner Anat
sform_code 1
sto_xyz:1 1.000000 0.000000 0.000000 -79.332245
sto_xyz:2 0.000000 1.000000 0.000000 -102.184464
sto_xyz:3 0.000000 0.000000 1.000000 -86.608360
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Left-to-Right
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
In accordance with the matrix determinant, the fslorient is said neurological for this image.
So my questions are:
1) How can I be sure that the s/q form is set correctly? I have access to the dicom and I tried looking at them using 3D Slicer but can't figure out what to do.
2) Is it OK to put together in a single analysis images that go from Left-to-Right and Right-to-Left and thus have different fslorient conventions?
Half my images are Left-to-Right oriented and the other half is Right-to-Left oriented when I look at their header after fslreorient2std. What am I to do?
I'm honestly really having a hard time understanding this issue...
Thank you
Shady
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