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 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
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