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Dear Helen,

you need to do something like

applytopup --imain=my_data --inindex=‘the direction that corresponds to blipup in your datain file’ --datain=my_acq_param.txt --topup=my_topup_results --method=jac --interp=spline --out=my_hifi_images

I agree that applytopup is quite cumbersome and I hope to replace it with something better at some stage.

Jesper

> On 3 Aug 2017, at 22:56, Helen Weng <[log in to unmask]> wrote:
> 
> Hello,
> 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).
> 
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
> 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.
> Helen