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
>>
--
“Well! I've often seen a cat without a grin,” thought Alice, “but a grin without a cat! It’s the most curious thing I ever saw in my life!” [Lewis Carroll, Alice in Wonderland]
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MRC Cognition and Brain Sciences Unit
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