HowToSetUpTopUp

In addition to the M0 set up in the previous page, you can set up two M0 images with inversed phase encoding direction as follows. This can be used for geometric distortion correction with FSL TopUp, as implemented in ExploreASL. The normal phase encoding direction should be identical to the phase encoding direction of the ASL scans. Then the inverted direction is along the same axis, but 'mirrored'/flipped.


1. Create your ASL protocol according to your needs. Make sure that the TR and TE are set to User Defined, so that they are not modified in step 2.

2. Copy that ASL sequence and set the number of repetitions to 1. Disable Background suppression and labeling.

3. In the Geometry tab, you should normally see AP as the fold-over direction (i.e., phase encoding is done AP). Just below it, the setting

"fat shift direction" (or something like that, I cannot remember right now) should read either A or P. Change it to whatever the opposite is. This is

what controls the phase reversal, and you only need one image to do this.