Most 3D wholebrain acquisitions are taken in the sagittal orientation. If your reference brain has a different orientation (i.e. the Colin Brain is in the axial orientation) than your single subject brain, you must Reorient the single subject brain to match the orientation of your reference brain. The non-linear registration described later cannot be run between two different orientation types.
- Check the header of your window, it will list the following information about your image: Viewer being used, the name of the file that was loaded, the orientation and the image size. In this case the orientation begins as Sagittal.
- Choose (Image Processing | Reorient/Crop Image)
- A new Image Processing Utility window will appear. Choose proper orientation (axial if using the Colin Brain). Click Reorient
- Click Copy Results to Image
- Save File (you cannot continue onto the Brain Extraction unless you save the current image). Click (File | Save)
- A new window will appear where you can type in your new filename and click Save.
- Once saved, the header of your window will display the new filename as well as the new orientation.