When we added the --spm-nii option, the problem disappears. The following thread is also relevant: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.html
On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald <mclaren.don...@gmail.com> wrote: > Thanks, that's what I thought might be happening. I'll check a few > different programs to see if I can recover the correct orientation. If > we need to reverse the images, would you recommend doing it before or > after the bbregister step? Would it be sufficient just to change the > header of the image or do we need to physically change the data? > > 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. > > > On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve > <gr...@nmr.mgh.harvard.edu> wrote: >> 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. 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