feedsRun

#!/usr/bin/env bash

set -e

outdir=$1
indir=$(pwd)

pushd ${outdir}

dti=${indir}/DTIap
dti_bvec=${indir}/DTIap.bvec
dti_bval=${indir}/DTIap.bval
dti_b=${outdir}/DTIapb #brain-extracted dti
dti_b0=${outdir}/DTIapb0
dti_u=${outdir}/DTIapu #undistorted dti
dti_b=${outdir}/DTIapb_mask #masked brain-extracted dti
dti_txt=${outdir}DTIap_acq_param.txt
dti_txt2=${outdir}/DTIap_index.txt

#create acq_param: dummies as we will not run TOPUP
printf "0 1 0 0.03388\n0 -1 0 0.03388\n" > $dti_txt

#create index files: all = 1 as we will not run TOPUP
nvol=$(fslnvols $dti)
indx=""
for ((i=1; i<=nvol; i+=1)); do indx="$indx 1"; done
echo $indx > $dti_txt2

fslroi $dti $dti_b0 0 1
bet $dti_b0 $dti_b -f 0.2 -R -n -m

eddy \
  --imain=$dti                  \
  --mask=$dti_b --acqp=$dti_txt \
  --index=$dti_txt2             \
  --bvecs=$dti_bvec             \
  --bvals=$dti_bval             \
  --repol                       \
  --out=$dti_u