Hi,
I recently used dcm2nii to convert DTI dicom data to nifti on a MacPPC. Upon
conversion i ran 'fslorient -getorient raw.nii.gz' and found that the file
was Radiological (which is what FSL likes). i then ran the 'fslhd' command
on the file to check the orientation matrix and i got this (RAS orientation):
qform_name Unknown
qform_code 0
qto_xyz:1 1.796875 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 1.796875 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 3.900000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
i then changed the sform using ' fslorient -setsformcode 1 raw.nii.gz' to
get the correct orientation (LAS) in the header :
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.796875 0.000000 -0.000000 0.000000
qto_xyz:2 0.000000 1.796875 -0.000000 0.000000
qto_xyz:3 0.000000 0.000000 3.900000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -1.796875 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 1.796875 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 3.900000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
The weird thing is that when i ran this same DTI dataset conversion on my
linux machine ,dcm2niigui produces the raw.nii.gz with the correct
orientation matrix (LAS) as above.
In summary, same dataset, converted using dcm2niiGUI , with the same .ini
settings, on different platforms produces different headers. Could someone
please suggest why this may be happening ?
More importantly:
In general, if the NIFTI header of a converted dicom image from the scanner
shows sform, qform as 'unknown' ,then is 'fslorient -setsformcode 1
raw.nii.gz' the correct solution ? Does it change the orientation of the
stored data in anyway?
Most importantly,
How does this affect the signs of b-vector array? i.e Would i have to negate
the signs of the bvec values if i change the sform? Thanks for your time.
Regards,
Vish
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