diff --git a/eddy/feedsRun.EddyHigh_b_Test b/eddy/feedsRun.EddyHigh_b_Test
index 7b238aa209f0adeb47af0e10a4336613f7b3b810..e04dd59ef869ba9c01ec03ee9e79ae97ac14a738 100755
--- a/eddy/feedsRun.EddyHigh_b_Test
+++ b/eddy/feedsRun.EddyHigh_b_Test
@@ -41,14 +41,14 @@ if [ ! -d "$indir" ]; then
 fi
 
 # Prepare arguments to pass to eddy
-eddy_args="--imain=${indir}/EddyHigh_b_TestData/eddyData/testData            " \
-          "--mask=${indir}/EddyHigh_b_TestData/eddyData/testMask             " \
-          "--bvals=${indir}/EddyHigh_b_TestData/eddyData/testBvals           " \
-          "--bvecs=${indir}/EddyHigh_b_TestData/eddyData/testBvecs           " \
-          "--index=${indir}/EddyHigh_b_TestData/eddyData/testIndex           " \
-          "--acqp=${indir}/EddyHigh_b_TestData/eddyData/testAcqparams        " \
-          "--topup=${indir}/EddyHigh_b_TestData/eddyData/testTopup           " \
-          "--nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose"
+eddy_args="--imain=${indir}/EddyHigh_b_TestData/eddyData/testData            
+           --mask=${indir}/EddyHigh_b_TestData/eddyData/testMask             
+           --bvals=${indir}/EddyHigh_b_TestData/eddyData/testBvals           
+           --bvecs=${indir}/EddyHigh_b_TestData/eddyData/testBvecs           
+           --index=${indir}/EddyHigh_b_TestData/eddyData/testIndex           
+           --acqp=${indir}/EddyHigh_b_TestData/eddyData/testAcqparams        
+           --topup=${indir}/EddyHigh_b_TestData/eddyData/testTopup           
+           --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose"
 
 # run eddy
 output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
diff --git a/eddy/feedsRun.EddyLSRTest b/eddy/feedsRun.EddyLSRTest
index d965a576635f64f9d5404a08a26747edfa73a23b..0e0fdaadf8a3e6ab039c4b8d4e6841087165db89 100755
--- a/eddy/feedsRun.EddyLSRTest
+++ b/eddy/feedsRun.EddyLSRTest
@@ -38,15 +38,15 @@ if [ ! -d "$indir" ]; then
 fi
 
 # Prepare arguments to pass to eddy
-eddy_args="--imain=${indir}/EddyLSRTestData/eddyData/testData         " \
-          "--mask=${indir}/EddyLSRTestData/eddyData/testMask          " \
-          "--bvals=${indir}/EddyLSRTestData/eddyData/testBvals        " \
-          "--bvecs=${indir}/EddyLSRTestData/eddyData/testBvecs        " \
-          "--index=${indir}/EddyLSRTestData/eddyData/testIndex        " \
-          "--acqp=${indir}/EddyLSRTestData/eddyData/testAcqparams     " \
-          "--topup=${indir}/EddyLSRTestData/eddyData/testTopup        " \
-          "--resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 " \
-          "--dont_peas --very_verbose"
+eddy_args="--imain=${indir}/EddyLSRTestData/eddyData/testData         
+           --mask=${indir}/EddyLSRTestData/eddyData/testMask          
+           --bvals=${indir}/EddyLSRTestData/eddyData/testBvals        
+           --bvecs=${indir}/EddyLSRTestData/eddyData/testBvecs        
+           --index=${indir}/EddyLSRTestData/eddyData/testIndex        
+           --acqp=${indir}/EddyLSRTestData/eddyData/testAcqparams     
+           --topup=${indir}/EddyLSRTestData/eddyData/testTopup        
+           --resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 
+           --dont_peas --very_verbose"
 
 # run eddy
 output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
diff --git a/eddy/feedsRun.EddyMBSTest b/eddy/feedsRun.EddyMBSTest
index babc78e2d436659921d20bc72ad68392e66b2201..273f2adf8c79cd393bbcef64caccc82c03cf597b 100755
--- a/eddy/feedsRun.EddyMBSTest
+++ b/eddy/feedsRun.EddyMBSTest
@@ -43,16 +43,16 @@ if [ ! -d "$indir" ]; then
 fi
 
 # Prepare arguments to pass to eddy
-eddy_args="--imain=${indir}/EddyMBSTestData/eddyData/testData            " \
-          "--acqp=${indir}/EddyMBSTestData/eddyData/testAcqparams        " \
-          "--mask=${indir}/EddyMBSTestData/eddyData/testMask             " \
-          "--index=${indir}/EddyMBSTestData/eddyData/testIndex           " \
-          "--bvecs=${indir}/EddyMBSTestData/eddyData/testBvecs           " \
-          "--bvals=${indir}/EddyMBSTestData/eddyData/testBvals           " \
-          "--topup=${indir}/EddyMBSTestData/eddyData/testTopup           " \
-          "--fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000               " \
-          "--flm=quadratic --dont_peas --estimate_move_by_susceptibility " \
-          "--mbs_niter=20 --mbs_lambda=10 --mbs_ksp=10 --very_verbose"
+eddy_args="--imain=${indir}/EddyMBSTestData/eddyData/testData            
+           --acqp=${indir}/EddyMBSTestData/eddyData/testAcqparams        
+           --mask=${indir}/EddyMBSTestData/eddyData/testMask             
+           --index=${indir}/EddyMBSTestData/eddyData/testIndex           
+           --bvecs=${indir}/EddyMBSTestData/eddyData/testBvecs           
+           --bvals=${indir}/EddyMBSTestData/eddyData/testBvals           
+           --topup=${indir}/EddyMBSTestData/eddyData/testTopup           
+           --fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000               
+           --flm=quadratic --dont_peas --estimate_move_by_susceptibility 
+           --mbs_niter=20 --mbs_lambda=10 --mbs_ksp=10 --very_verbose"
 
 # run eddy
 output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
diff --git a/eddy/feedsRun.EddyS2VTest b/eddy/feedsRun.EddyS2VTest
index a511d5d4bda6edebb1d357c60b4fb8b10c87f4a8..c2ae8867bc510ab5125f8d4f26b3518347424656 100755
--- a/eddy/feedsRun.EddyS2VTest
+++ b/eddy/feedsRun.EddyS2VTest
@@ -40,17 +40,17 @@ if [ ! -d "$indir" ]; then
 fi
 
 # Prepare arguments to pass to eddy
-eddy_args="--imain=${indir}/EddyS2VTestData/eddyData/testData     " \
-          "--mask=${indir}/EddyS2VTestData/eddyData/testMask      " \
-          "--bvals=${indir}/EddyS2VTestData/eddyData/testBvals    " \
-          "--bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs    " \
-          "--index=${indir}/EddyS2VTestData/eddyData/testIndex    " \
-          "--acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams " \
-          "--repol --ol_type=slice --ol_nstd=6 --ol_nvox=500      " \
-          "--niter=8 --fwhm=10,6,4,2,0,0,0,0 --nvoxhp=5000        " \
-          "--mporder=16 --s2v_niter=10 --s2v_interp=trilinear     " \
-          "--s2v_lambda=1 --very_verbose                          " \
-          "--slspec=${indir}/EddyS2VTestData/eddyData/testSlspec  "
+eddy_args="--imain=${indir}/EddyS2VTestData/eddyData/testData     
+           --mask=${indir}/EddyS2VTestData/eddyData/testMask      
+           --bvals=${indir}/EddyS2VTestData/eddyData/testBvals    
+           --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs    
+           --index=${indir}/EddyS2VTestData/eddyData/testIndex    
+           --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams 
+           --repol --ol_type=slice --ol_nstd=6 --ol_nvox=500      
+           --niter=8 --fwhm=10,6,4,2,0,0,0,0 --nvoxhp=5000        
+           --mporder=16 --s2v_niter=10 --s2v_interp=trilinear     
+           --s2v_lambda=1 --very_verbose                          
+           --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec  "
 
 # run eddy
 output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
diff --git a/eddy/feedsRun.EddyTest b/eddy/feedsRun.EddyTest
index c50ac5e39f2a29a79c8274f509b94171f29f3a0a..3c0d2b23e23944fa69af129cbe4454a5d4ba8559 100755
--- a/eddy/feedsRun.EddyTest
+++ b/eddy/feedsRun.EddyTest
@@ -37,13 +37,13 @@ if [ ! -d "$indir" ]; then
 fi
 
 # Prepare arguments to pass to eddy
-eddy_args="--imain=${indir}/EddyTestData/eddyData/testData     " \
-          "--mask=${indir}/EddyTestData/eddyData/testMask      " \
-          "--bvals=${indir}/EddyTestData/eddyData/testBvals    " \
-          "--bvecs=${indir}/EddyTestData/eddyData/testBvecs    " \
-          "--index=${indir}/EddyTestData/eddyData/testIndex    " \
-          "--acqp=${indir}/EddyTestData/eddyData/testAcqparams " \
-          "--repol --fwhm=10,0,0,0,0 --dfields -v"
+eddy_args="--imain=${indir}/EddyTestData/eddyData/testData 
+           --mask=${indir}/EddyTestData/eddyData/testMask 
+           --bvals=${indir}/EddyTestData/eddyData/testBvals 
+           --bvecs=${indir}/EddyTestData/eddyData/testBvecs 
+           --index=${indir}/EddyTestData/eddyData/testIndex 
+           --acqp=${indir}/EddyTestData/eddyData/testAcqparams 
+           --repol --fwhm=10,0,0,0,0 --dfields -v"
 
 # run eddy
 output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
diff --git a/eddy/runEddy b/eddy/runEddy
index 10531b41def40e247cd4813af605655e6b956c7c..28f5c371045e754ed7185de935a81f08667cdbee 100755
--- a/eddy/runEddy
+++ b/eddy/runEddy
@@ -57,7 +57,7 @@ for cuda_exe in ${cuda_exes};
 do
   tmp=`basename ${cuda_exe}`
   variant=`echo ${tmp} | sed 's/eddy_//'`
-  jid=`fsl_sub -l ${odir} -q cuda.q ${cuda_exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
+  jid=`fsl_sub -l ${outdir} -q cuda.q ${cuda_exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
   cuda_jids="${cuda_jids} ${jid}"
 done
 
@@ -66,7 +66,7 @@ for cpu_exe in ${cpu_exes};
 do
   tmp=`basename ${cuda_exe}`
   variant=`echo ${tmp} | sed 's/eddy_//'`
-  jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
+  jid=`fsl_sub -l ${outdir} -q long.q -s openmp,6 ${cpu_exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
   cpu_jids="${cpu_jids} ${jid}"
 done
 
@@ -108,7 +108,7 @@ for exe in ${cuda_exes} ${cpu_exes};
 do
   tmp=`basename ${cuda_exe}`
   variant=`echo ${tmp} | sed 's/eddy_//'`
-  prefix="${odir}/eddyOutput_${variant}"
+  prefix="${outdir}/eddyOutput_${variant}"
   outputs="${outputs} ${prefix}"
   if [ ! -f ${prefix}.nii* ]; then
     echo "${prefix} is missing"