Good morning,
When I open a T1 volume (see header info below) into FSLview, the images are
not displayed correctly:
the anterior posterior axis is incorrect, the label p pointing to the
front of the brain and the label a pointing to the back of the brain;
the superior- inferior axis is correct but the images are shown upside
down in the FSLview window (top of the brain at the bottom of the window);
the left right axis is correct.
I tried to correct this using avsswapdim but without success. I can get the
images to show the right way up but then the L R axis becomes incorrect.
The ant post never changes.
The volume is in radiological orientation. Its original format was DICOM and
was transformed into nii format using a two-step procedure: first into minc
(using NeuroLens), and then into nii (using the mri_convert command in
FreeSurfer). For some reason, when I initially converted DICOM images
directly into nii with the FreeSurfer command, FSL did not recognize the
final output as a valid volume.
I would appreciate any input on how to address this issue. Thank you.
Regards
Olivier Piguet
filename T1new.nii
sizeof_hdr 348
data_type INT16
dim0 3
dim1 256
dim2 180
dim3 256
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 348
cal_max 0.0000
cal_min 0.0000
scl_slope 0.000000
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 -1.000000 0.000000 -0.000000 128.000000
qto_xyz:2 0.000000 -1.000000 -0.000000 -94.272400
qto_xyz:3 0.000000 0.000000 -1.000000 105.256042
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
qform_zorient Superior-to-Inferior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -1.000000 0.000000 -0.000000 128.000000
sto_xyz:2 -0.000000 -1.000000 -0.000000 -94.272400
sto_xyz:3 0.000000 0.000000 -1.000000 105.256042
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Anterior-to-Posterior
sform_zorient Superior-to-Inferior
file_type NIFTI-1+
file_code 1
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