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. Author manuscript; available in PMC: 2018 Oct 20.
Published in final edited form as: Curr Protoc Mol Biol. 2017 Jul 5;119:29A.5.1–29A.5.38. doi: 10.1002/cpmb.40

Figure 6. Correcting misalignment artifacts artifact for averaging whole head images using FLIRT in FSL.

Figure 6.

FSL FLIRT is a rigid body alignment tool that can correct movement artifacts (Step A4 and Troubleshooting). One of four offset images was randomly chosen to serve as a reference to perform an affine rigid body rotation with FSL FLIRT on the other three images as well as to itself (Step A4 and Troubleshooting). Show in the box at top left is the GUI and the window that is activated when selecting “FLIRT linear registration” in the GUI (indicated by red arrow). IN the pop-up window, select “Rigid Body”(6 parameter model). This procedure aligned all of the images together. This tool can also be used for alignments leading to the MDA (Step B3), but we prefer to do that step in NiftiReg.