How to check image orientation

RABIES assumes input data is oriented according to the NIfTI standard (RAS+, i.e. Right–Anterior–Superior). Incorrectly oriented images are one of the most common causes of registration failure and of results that look wrong for no apparent reason, because the ANTs/ITK tools RABIES calls will happily register a mis-oriented brain to the template and produce nonsense.

Important

Check orientation before you report a bug, and before you start troubleshooting anything else. It costs five minutes and rules out the most likely explanation.

Check with ITK-SNAP

ITK-SNAP is a free, open-source medical image viewer that reads NIfTI orientation information correctly. Other viewers do not always, which is why it is the recommended tool here.

  1. Open your image. File → Open Main Image…, and load your NIfTI anatomical scan.

  2. Check the anatomy is where you expect it. ITK-SNAP shows axial, coronal and sagittal views. The nose should be anterior, the top of the head superior.

  3. Compare against your reference template. Open the atlas you intend to pass to --anat_template (SIGMA, DSURQE, Fischer rat, whichever applies) in a second ITK-SNAP window. Structures should appear in similar positions, and the orientation labels should match.

  4. Check the orientation labels. Each view is labelled R/L, A/P and S/I. Confirm each corresponds to the real anatomical direction in your scan, then move the cursor: the crosshair should track consistently across all three views, so that dragging towards the label R moves towards anatomical right.

If any of these disagree, the orientation stored in your NIfTI header does not describe your data, and you need to fix it before running RABIES. This is usually introduced during conversion from the scanner format.

See also

For Bruker data, BrkRaw handles the raw-to-NIfTI conversion; the CoBrALab maintains notes on the conversion.

If orientation is correct and registration still fails

Move on to How to troubleshoot registration, which covers tuning inhomogeneity correction, masking and registration stages. Read the preprocessing QC report first, to establish which registration step is the one that failed.

When you do report a problem, follow the issue template.