FAQS

Distortion correction

We recommend using FSL's Topup. An example pipeline for running topup is given on https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup Note that it is not usually necessary to calculate the readout duration (and look for parameters such as the ETL and echo spacing), because all our topup images are matched in terms of readout length to the functional or diffusion scan they are used to correct. Hence, providing a readout length of '1' will generate warp field in units of voxels rather than mm. These can be equally well to undistort the images, in exactly the same way as in the ApplyTopup example.