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My best guess is that the images themselves were actually acquired in different orientations - or the order in which the voxels are stored is different. This is the only thing I can think of that would cause this result if the matrices in the headers are identical between the two scans. best regards, -John On Wednesday 09 July 2008 23:06, Cameron Craddock wrote: > Hello all, > > > > I have some fMRI data that was reconstructed offline and all of the spatial > location information is lost in the process. Previously I have been able > to copy this information from another scan that is acquired during the same > session with the same slice prescription using the following script. > > > > M0=spm_get_space(file_with_good_center); > > spm_get_space(file_with_bad_center,M0); > > > > I am using nifti files. > > > > I have recently upgraded my Matlab version and installed the latest SPM > patches and now this procedure no longer works in two ways: > > > > 1). The location mat is only changed for the first volume in the 4D nifti > files. This is easily corrected using a loop. > > 2). The image orientation after this procedure is not correct. Attached is > a screen capture from spm. I copied the mat information from the top image > to the bottom image. I have verified that the mat information in the > headers are the same by using spm_vol. I have also verified the header > information using AFNI's 3dinfo. AFNI also shows the images in the same > manner as SPM. > > > > Is there some other header information that I need to modify to get this to > work correctly? Is there another method that I could use that might work? > > > > Thanks in advance for any and all comments. > > > > > > Here is my system information: > > > > RHEL 5.0 running on quadcore intel Xeon 64bit > > Matlab 2008a > > SPM5 with Updates_1782 > > I have recompiled SPM and haven't had any other problems. > > > > Regards, > > Cameron Craddock