Hello,
In general, if the sform/qform codes are set, then it is safe to assume that dicom-to-nifti conversion has worked correctly, an unset sform/qform code would be cause for concern. It is normally fine to use both neurological and radiological data - with the exception of some low-level operations like fslmerge. If you are unsure, you can use the combination of fslswapdim/fslorient to set all your data in the same orientation.
hope this helps,
Kind Regards
Matthew
> On 29 Jun 2016, at 13:07, Shady Rahayel <[log in to unmask]> wrote:
>
> 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
