acqparams_maker

Summary

The acqparams.txt describes phase encoding direction and TotalReadoutTime of dwi. It is required to correct susceptibility distortion of epi using FSL's topup.

This script automatically creates acqparams.txt using json files which is made by dcm2niix.

DWI files of reversed encoding directions are required for topup.

If you want to run topup without a file of reversed encoding direction, you may want to check Synb0-DISCO.

Prerequisite

DWI.json (from dcm2niix)

Instructions

examples

# If you have only one phase encoding direction, this will make an acqparams.txt
# for Synb0-DISCO pipeline.
s_acqparams_maker dwi.json

# If you have reversed phase encoding directions, this will make an acqparams.txt
# for topup.
s_acqparams_maker dwi_AP.json dwi_PA.json

# If you want to use more than one b0 for each phase encoding directions
s_acqparams_maker dwi_AP.json dwi_PA.json 3 3 # 3 b0s for each direction