Applying TopUp to functional images

Hi all!
We have obtained PEPOLAR images to apply topup to functional images. The problem is that: all the instructions I’ve seen so far used only one datain file. However, the total readout time in the functional images are different than fieldmap runs, therefore we think we need to use another datain file for the applytopup command. Do you have any idea how should it be?

Currently it is like this (which does not feel right)
topup --imain=${derivatives}/sub-${subjID}/ses-${sessNum}/fmap/mergedAP_PA –datain=${derivatives}/sub-${subjID}/ses-${sessNum}/fmap/datain.txt --config=b02b0.cnf --out=${derivatives}/sub-${subjID}/ses-${sessNum}/fmap/topup_ses-${sessNum}

applytopup --imain=${niidir}/sub-${subjID}/${funcfile} --inindex=1 --method=jac –datain=${derivatives}/sub-${subjID}/ses-${sessNum}/fmap/datain.txt --topup=${derivatives}/sub-${subjID}/ses-${sessNum}/fmap/topup_ses-${sessNum} --out=${derivatives}/sub-${subjID}/$unwarped

Thanks in advance!