Hi all
an old friend; orientation.
The FAQ says
"FSLVIEW always displays images "radiologically". Hence, any
"neurologically" ordered nifti image will be flipped in the (voxel) x-
axis when it is displayed in FSLVIEW. FSLVIEW also now labels the
axes (e.g. L, R, P, A, I, S - Left, Right, Posterior, Anterior,
Inferior, Superior). In the case of oblique acquisitions it chooses
the "closest" axis label."
I have a DICOM image which I have converted to Analyze (with SPM2)
and NIFTI (with
the LONI debabeler). The Analyze image is in RADIOLOGICAL order
and the
NIFTI in NEUROLOGICAL order. Viz:
% avworient -getorient 0001.nii
NEUROLOGICAL
% avworient -getorient 0001-spm2.hdr
RADIOLOGICAL
and I have attached the headers (from avwhd)
Display
-----------
Now when I display these images, the analyze one displays
as I expect with R on the left of the screen, P on the bottom, S on
the top.
However, the NIFTI image is oriented rather strangely with R to
the right of the screen, P to the top and S to the top (ok). In
light of the above
quote, I expected FSLVIEW to display the image in the same orientation
as the analyze image (or at least with respect to R and L; I tried
to attach
screen shots but the message was rejected as too large)
The labels in both cases are correct in the sense that R is next to
the right side of the brain
(I know which side of the brain is right for this person).
Can you comment ?
Header
-----------
I am also a bit puzzled by the coordinates. This is probably not
your group's bother, as the conversions
are done by SPM and LONI, but I am using FSLVIEW to measure the
coordinates.
For the analyze image we have
Right to Left: x pixel coordinate increasing 0->63
and x physical coordinate decreasing 111.56->-95.16 (dx=206.72)
Posterior to Anterior: y pixel coordinate increasing 0->63 and y
physical coordinate increasing -95.16->111.56 (dy=206.72)
Inferior to Superior: z pixel coordinate increasing 0->28 and z
physical coordinate increasing -30->110 (dz=140)
For the nifti image we have
Right to Left: x pixel coordinate increasing 0->63
and x physical coordinate decreasing 638.14->431.42 (dx=206.72)
Posterior to Anterior: y pixel coordinate decreasing 63->0 and y
physical coordinate increasing 434.02->640.35 (dy=206.33, z=14)
Inferior to Superior: z pixel coordinate increasing 0->28 and z
physical coordinate increasing 5.09->144.83 (dz=139.74,y=31)
So what we see here is that :
- Right to Left is consistent from Analyze to Nifti
- Posterior to Anterior is pixel coordinate flipped from Analyze
to Nifti
- Inferior to Superior is consistent from Analyze to Nifti
But
- Physical coordinates are offset between analyze and nifti
- The nifti coordinates show that the Y and the Z axes are
coupled (i.e. z changes if I change y and vice versa).
I didn't expect this and if Y is coupled to Z, I would expect X
to be coupled also (it's not).
If you have any thoughts in this I would be interested. I will also
contact the LONI folks.
regards
Neil
filename 0001-spm2.hdr
sizeof_hdr 348
data_type dsr
db_name fghhjjkkll-0018-0
extents 0
session_error 0
regular r
hkey_un0
dim0 4
dim1 64
dim2 64
dim3 29
dim4 1
dim5 0
dim6 0
dim7 0
vox_units mm
cal_units
unused1 0
datatype 4
bitpix 16
pixdim0 0.0000000000
pixdim1 3.2812500000
pixdim2 3.2812500000
pixdim3 5.0000000000
pixdim4 1.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 0.0000
funused1 0.0558
funused2 0.0000
funused3 0.0000
cal_max 1829.0000
cal_min -1829.0558
compressed 0
verified 0
glmax 32767
glmin -32768
descrip 3T 2D SE\EP TR=2000ms/TE=40ms/FA=90deg 23-Oct-2006 15:28:4.2875 Mosaic
aux_file
orient 0
originator #
origin1 35
origin2 30
origin3 7
generated today
scannum
patient_id
exp_date
exp_time
hist_un0
views 0
vols_added 0
start_field 0
field_skip 0
omax 0
omin 0
smin 0
smin 0
file_type ANALYZE-7.5
file_code 0
Byte swapping
filename 0001.nii
sizeof_hdr 348
data_type INT16
dim0 3
dim1 64
dim2 64
dim3 29
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units Unknown
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 3.2812500000
pixdim2 3.2812500000
pixdim3 5.0000000000
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 -3.281250 0.000000 -0.000000 638.135620
qto_xyz:2 0.000000 -3.275130 -0.305243 644.623718
qto_xyz:3 -0.000000 -0.200316 4.990674 11.303008
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
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
aux_file
|
