Dear Mark,
are you using the latest version of FSL/topup? This is a known bug, but it has been fixed and as far as I can tell that fix is in the latest release.
Jesper
On 5 Aug 2014, at 13:47, Mark Pinsk <[log in to unmask]> wrote:
> Hi Jesper et al.
>
> I noticed that orientation and matrix information does not carry over from the topup input to its output (the iout and fout outputs). I noticed the orientation labels are gone when viewing the outputs in fslview. When comparing the headers with fslhd I noticed these fields are missing from the iout and fout outputs. Is there a reason for this? I can paste them back into the files with fsledithd, but that's a bit cumbersome. This doesn't happen with the fieldcoeff output, just the iout and fout.
>
> Thanks,
> Mark
>
>
> Missing fields:
> qform_code = '1'
> qform_code_name = 'Scanner Anat'
> qto_xyz_matrix = '2 0 0 96 0 2 0 96 0 0 2 50 0 0 0 1'
> qto_ijk_matrix = '0.5 0 0 -48 0 0.5 0 -48 0 0 0.5 -25 0 0 0 1'
> quatern_b = '0'
> quatern_c = '0'
> quatern_d = '0'
> qoffset_x = '96'
> qoffset_y = '96'
> qoffset_z = '50'
> qfac = '1'
> qform_i_orientation = 'Left-to-Right'
> qform_j_orientation = 'Posterior-to-Anterior'
> qform_k_orientation = 'Inferior-to-Superior'
> sform_code = '1'
> sform_code_name = 'Scanner Anat'
> sto_xyz_matrix = '1 0 0 96 0 1 0 96 0 0 1 50 0 0 0 1'
> sto_ijk matrix = '1 0 0 -96 0 1 0 -96 0 0 1 -50 0 0 0 1'
> sform_i_orientation = 'Left-to-Right'
> sform_j_orientation = 'Posterior-to-Anterior'
> sform_k_orientation = 'Inferior-to-Superior'
> num_ext = '0'
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