After successfully running topup and applytopup, I noticed the orientation, qform and sform of all the results differ from the input volume, and the qform_code and sform_code are all zero (!?).
The command was:
topup --imain=topup_in.nii --datain=topup_params.txt --out=topup_out --fout=topup_fout --iout=topup_iout
and the Qforms & Sforms are:
QFORM
-2.0 0.0 0.0 129.2 0.0 2.0 0.0 -116.9 0.0 0.0 2.0 -39.9 0.0 0.0 0.0 1.0 topup_in.nii
2.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 1.0 topup_fout.nii
2.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 1.0 topup_iout.nii
5.0 0.0 0.0 128.0 0.0 5.0 0.0 128.0 0.0 0.0 5.0 73.0 0.0 0.0 0.0 1.0 topup_out_fieldcoef.nii
SFORM
-2.0 0.0 0.0 129.2 0.0 2.0 0.0 -116.9 0.0 0.0 2.0 -39.9 0.0 0.0 0.0 1.0 topup_in.nii
-2.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 1.0 topup_fout.nii
-2.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 1.0 topup_iout.nii
1.0 0.0 0.0 128.0 0.0 1.0 0.0 128.0 0.0 0.0 1.0 73.0 0.0 0.0 0.0 1.0 topup_out_fieldcoef.nii
ORIENT
RPI topup_in.nii
LPI topup_fout.nii
LPI topup_iout.nii
LPI topup_out_fieldcoef.nii
Note also that the result files have Sforms different from their own Qforms. And none of them have sensible origins. Is it correct to just use fslcpgeom to fix the headers?
And what would be correct for the "fieldcoef" result, since it has a different grid size?
Mark.
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