Dear Matt,
I tried to remove oblique sforms (using fslcreatehd) and re-run
freesurfer. But something is wrong, as my Fs thickness data are very
different and there is still misalignment of my volume and surface
images in Caret.
Which parameters exactly should be changed in the header of the t1 and
t2 images? I am confused about the exact number that should be used for
the sform_code and qform_code or other parameters.
Please find below an output of the original t1.nii header. Thanks for
your help!
Best,
Ruthger
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 170
dim2 240
dim3 240
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 0.9999969602
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 0.0089999996
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -0.995361 -0.087172 0.040628 84.904289
qto_xyz:2 -0.090758 0.991145 -0.096925 -55.609478
qto_xyz:3 0.031819 0.100163 0.994462 -135.906647
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 -0.995361 -0.087172 0.040629 84.904305
sto_xyz:2 -0.090759 0.991145 -0.096925 -55.609467
sto_xyz:3 0.031820 0.100163 0.994462 -135.906647
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+
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