Dear SPM experts,
I have two problems related to Left and Right issue with using SPM .
I am using both SPM2 and SPM5. In both version I have set
defaults.analyze.flip = 0 in spm_default.m
flip = 0 in spm_flip_analyze_images.m
The first problem is that I find same dicom files converted by SPM2 (dicom
conversion toolbox) and SPM5 have opposite x step, see attached screen shot
from SPM5 display.
The second problem I have is when I do segmentation with SPM5. I have input
image in nifit format and the head is
V1 =
fname: 'rT199_brain.nii'
mat: [4x4 double]
dim: [512 512 53]
dt: [16 0]
pinfo: [3x1 double]
n: [1 1]
descrip: 'FSL3.2beta'
private: [1x1 nifti]
>>V1.mat
ans =
0.4688 0 0 -120.2346
0 0.4688 0 -120.2344
0 0 3.0000 -81.0000
0 0 0 1.0000
So it's three dimesion all have positive step and check with SPM5 display
its left is left and right is right (neurological, x increase from left to
right). However after segmentation I have the normalised segmented image
with x dimension has negative step:
V2=spm_vol('wc1rT199_brain.nii')
V2 =
fname: 'wc1rT199_brain.nii'
mat: [4x4 double]
dim: [91 109 91]
dt: [2 0]
pinfo: [3x1 double]
n: [1 1]
descrip: 'spm - 3D normalized'
private: [1x1 nifti]
>>V2.mat
ans =
-2 0 0 92
0 2 0 -128
0 0 2 -74
0 0 0 1
When I display it using SPM5, the image itself appears that left is left and
right is right. However, I wonder it was flipped because now x increases
from right to the left!
I have a few questions:
1. What value should we set for "flip" in "spm_default.m" and
"spm_flip_analyze_images.m" for SPM2 and SPM5, if we directly import images
from dicom file?
2. Why SPM2 and SPM5 convert image in different orientation (I mean lefe and
right)?
3. What orientation (positive x step or negative x step, neurological or
radiological) should use for nifit file, if we import nifit file to SPM5? I
check SPM5 templates and they all have negative voxel size in x.
I should be very much appreciated for the help from you.
Jian
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