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