#!/bin/bash

for i in 20S*.tif
do
   echo $i

   motioncor2 -InTiff "$i" -OutMrc aligned_MotionCor2/"${i/.tif/.mrc}" -Gain SuperRef_20S_000_Mar28_14.49.23.mrc -FtBin 2 -Patch 9 9 -Bft 300 -kV 300 -PixSize 0.53 -FmDose 1.0 -Throw 2 -Gpu 1 | tee aligned_MotionCor2/"${i/.tif/}_DriftCorr.log" 
done