We found a problem in writing Analyze format data. In particular, we were not writing the correct data_history orientation information, even though the .mat file was being written correctly.
Since Freesurfer uses the .mat file if present, Freesurfer will not be affected by this bug. The problem is restricted to the case of using non-Freesurfer software to view or process Analyze data exported by Freesurfer.
A new version of mri_convert fixes this bug. We're not releasing updates for the rest of the Freesurfer binaries that write data (and will write the incorrect Analyze volumes) in the interest of space, so if you are exporting Analyze data for use outside of Freesurfer, please use mri_convert as a final step.
Thanks to Darren Weber and Graham Wideman for Analyze format information.
Please see the README in the archive for more details.
Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_convert-20041216-Linux.tar.gz
Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_convert-20041216-Darwin.tar.gz