Hi Donald, it might be the case. If the fmri has an ordering such that
the columns increase as you go from left to right, then they will have
to be reversed when you map them to the orig.mgz. This is generally not
a problem because we always keep track of which side is left and right.
If you are using a visualization tool that does not read in and act on
the geometry, then things can appear to flip around.
doug
On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
Dear All,
I've noticed something strange with some data I'm helping to process:
When looking at the L/R asymmetry in the brains (attached), the images
seem to flip after bbregister/mri_vol2vol. The exact commands:
bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2
mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg
register.dat --no-resample --o transformed_fMRI.nii
I've attached a document that shows the flipping. You'll notice the
highest point of the ventricle flips sides after
bbregister/mri_vol2vol. Any thoughts on what is going on would be
appreciated.
The contents of register.dat are as follows:
FS_D011
3.000000
3.540000
0.150000
-9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02
1.619825601577759e+00
6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01
-1.230294322967529e+01
4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01
-1.072110843658447e+01
0 0 0 1
round
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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