I have just discovered a small bug in the NIFTI reader in FreeSurfer. The bug caused the sform/qfrom matrix to be slightly off for oblique volumes that are non-isotropic (the more oblique and the more non-isotropic, the worse). Part of the error involves the matrix being slightly non-orthogonal.

There is NO effect of this bug if any of the following apply: 1. You use mri_convert to convert from DICOM (or any other non-NIFTI format) to NIFTI 2. Your volumes are not oblique 3. Your volumes are isotropic

This bug can manifest itself only when using NIFTI as input to a freesurfer tool.

I have fixed this bug in both our DEV and STABLE versions.

doug