I am setting up a pipeline for fieldmap correction of EPI images, using 2 blip images (blipup and blipdown) with topup and applytopup.
Can someone explain how to use applytopup to correct EPI images with the output from topup? I am confused by the --imain argument, where the example has inputing 2 sets of images, one with positive PE and one with negative PE. In my EPI images to be corrected, all are collected in the positive PE direction. There is nothing I can input for the negative direction. The 2 blipup/blipdown images are collected in opposite PE directions (blipup = positive, blipdown = negative).
applytopup --imain=blip_down,blip_up --inindex=2,1 --datatin=my_acq_param.txt --topup=my_topup_results --out=my_hifi_images
Thanks for any clarification about how to correct EPI images collected in the positive PE direction.