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It means that one of your images is shifted. If you applied the same transforms to all images, then you should end up with the same image dimension and location. Since the same process results in 2 different values, it means that you changed the images in PVELAB somehow OR you didn't apply the same transforms to all images. I would look more closely at PVELAB to see why its shifting some of the images. As Bas said, try to avoid using ANALYZE format images as they don't contain the necessary information. 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 Wed, Jan 30, 2013 at 8:39 AM, Pieter Vandemaele <[log in to unmask]> wrote: > Dear all, > > I want to do an anova analysis with 2 factors, age(young/old) and corrected > (yes/no). > In fact, all images are processed until normalisation. Then all images are > converted to Analyze and processed in another program (PVELAB) and converted > back to Nifti and smoothed. > The original images are also converted back Nifti and smoothed so all images > underwent the same transformation. > The corrected and uncorrected images are then used in the Anova. > > I got the following error running the Anova module in spm_check_orientations > > Running 'Factorial design specification' > Mapping files : > ** The images do not all have same orientation and/or voxel sizes. ** > The function assumes that a voxel in one image corresponds exactly > with the same voxel in another. This is not a safe assumption if > the orientation information in the headers or .mat files says that > the images are oriented differently. Please ensure that you process > all data correctly. For example, you may have realigned the images, > but not actually resliced them to be in voxel-wise alignment. > Here are the orientation matrices of the image volumes. This list > can be used to determine which file(s) are causing the problem. > [-2 0 0 80; 0 2 0 -114; 0 0 2 -52] file 1 > [-2 0 0 80; 0 2 0 -114; 0 0 2 -53] file 2 > > I now show only the difference between corrected and uncorrected in the > factorial design. > Is this due to rounding errors like mentioned in > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0708&L=SPM&P=R35432&I=-3&d=No+Match%3BMatch%3BMatches > How can I correct for this, what is the meaning of -52 and -53? > Are > Regards > > Pieter