Currently, total readout time (necessary for FSL's topup config file) is fetched in separate_b0_and_dwi from the .json metafile of the DWI image. Then it has to be manually passed as an input argument to the prepare_topup_file.
The prepare_topup_file script works only with b0 images which do not have .json metafiles, thus the prepare_topup_file itself cannot easily fetch total readout time.
Possible solution would be to combine both scripts into single one.
Currently, total readout time (necessary for FSL's topup config file) is fetched in separate_b0_and_dwi from the .json metafile of the DWI image. Then it has to be manually passed as an input argument to the prepare_topup_file. The
prepare_topup_filescript works only with b0 images which do not have .json metafiles, thus theprepare_topup_fileitself cannot easily fetch total readout time.Possible solution would be to combine both scripts into single one.