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Has anyone reported this problem to Chris Rorden for investigation? Why should dcm2nii yield different q/s forms in the first place? cheers, -Mike H. On Thu, 2010-03-11 at 00:03 +0000, Martin M Monti wrote: > Hi Jenifer, > > I have had the same problem; after using dcm2nii. > I've resolved it in 2 steps > > (1) use the -deleteorient option in fslorient (this should get rid of > the problem) > (2) flip the image: fslswapdim -x y z (I think it's -x to invert left-right) > > In my case, I have a small capsule that clearly showed that right and > left got inverted after deleting the s/qform. > I can't vouch whether that would be the case for your images too, but > that's my experience. > > Perhaps you could scan 1 more person and put a small marker by one side > of their head (e.g. a cashew!), so you can check? > > cheers > > Martin > > Mark Jenkinson wrote: > > 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 > >> >