They may both be correct. See how the images appear if you do a Check
reg. If all is well, the SPM5 should show them both in alignment.
Best regards,
-John
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On Behalf Of Jeong Bum Seok
Sent: Wednesday, November 15, 2006 11:47 PM
To: [log in to unmask]
Subject: [SPM] how coronally acquired images are rotated to axial
My EPI data were acquired coronally.
And I'd like to rotate axially with display function in SPM5.
If I type 2 in pitch in display, it looks like axial image.
But header information is like below. y axis orientation is superior to
inferior.
If I use avwswapdim of fsl function, it also looks like axial image.
And header images is like below.
Which one is correct? and let me know what is correct method to rotate
it
correctly
Thank you for advance
# by spm5
filename I007.hdr
sizeof_hdr 348
data_type INT16
dim0 3
dim1 64
dim2 64
dim3 24
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 3.7500000000
pixdim2 3.7500000000
pixdim3 6.0000000000
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 0
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 Aligned Anat
qform_code 2
qto_xyz:1 -3.750000 -0.000000 -0.000000 118.125000
qto_xyz:2 0.000000 -1.560551 5.455784 -13.584177
qto_xyz:3 0.000000 -3.409865 -2.496881 136.124893
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Superior-to-Inferior
qform_zorient Posterior-to-Anterior
sform_name Aligned Anat
sform_code 2
sto_xyz:1 -3.750000 0.000000 0.000000 118.125000
sto_xyz:2 0.000000 -1.560551 5.455785 -13.584177
sto_xyz:3 0.000000 -3.409865 -2.496881 136.124893
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Superior-to-Inferior
sform_zorient Posterior-to-Anterior
file_type NIFTI-1
file_code 2
descrip units specified
# by FSL
filename test1.nii
sizeof_hdr 348
data_type INT16
dim0 3
dim1 64
dim2 24
dim3 64
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 3.7500000000
pixdim2 6.0000000000
pixdim3 3.7500000000
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
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 Unknown
qform_code 0
qto_xyz:1 3.750000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 6.000000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 3.750000 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
descrip FSL3.3
|