Oh, right, that can be a problem. In 5.2, I've changed it to use nii by default. This breaks when spm2 is used, but then the user can spec to use img instead. doug
On 12/19/12 5:38 PM, MCLAREN, Donald wrote: > 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. If you have received this e-mail >>> unintentionally, please immediately notify the sender via telephone at (773) >>> 406-2464 or email. >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . 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