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Hi, As Matt says, you really will only know the left-right orientation if you have some markers in the image. I suspect that your sform is actually the correct one as the (0,0,0) mm is within the FOV based on the sform but not for the qform. However, this really is not very trustworthy. You could also view the original DICOM and try to check the left-right orientation that way. All the best, Mark On 10 Mar 2010, at 19:52, Matt Glasser wrote: > Hi Jenifer, > > What software did you use to convert this data to NIFTI? Do you > have any > fiducial marker on the data that lets you know what is left and what > was > right? > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf > Of Jenifer Juranek > Sent: Wednesday, March 10, 2010 1:47 PM > To: [log in to unmask] > Subject: [FSL] inconsistent left-right order stored in sform and qform > > I came across the following warning while working with some (but not > all) GE > T1 and T2 data: > "inconsistent left-right order stored in sform and qform in file "... > "Using sform instead of qform values" > > The dicom data were run through dcm2nii before opening in FSLview. > Subjects with the warning do demonstrate a discrepancy between qform > and > sform matrices. > > Should I be concerned about this warning? > If I remember correctly, GE scanners used to be susceptible to L-R > orientation being dependent on what the scanner operator did at the > time of > acquisition. Is this still true? > > Any comments are greatly appreciated. > Jenifer > > The fslhd info (tail of the file) for subjects with this warning is > appended > below: > qform_name Scanner Anat > qform_code 1 > qto_xyz:1 0.937500 0.000000 -0.000000 -116.604500 > qto_xyz:2 0.000000 1.500000 -0.000000 -73.582993 > qto_xyz:3 0.000000 0.000000 -0.937500 -113.845497 > qto_xyz:4 0.000000 0.000000 0.000000 1.000000 > qform_xorient Left-to-Right > qform_yorient Posterior-to-Anterior > qform_zorient Superior-to-Inferior > sform_name Scanner Anat > sform_code 1 > sto_xyz:1 0.937500 0.000000 0.000000 -116.604500 > sto_xyz:2 0.000000 1.500000 0.000000 -73.582993 > sto_xyz:3 0.000000 0.000000 0.937500 -113.845497 > 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 > file_type NIFTI-1+ > file_code 1 > descrip > aux_file >