diff --git a/eddy/feedsRun.EddyHigh_b_Test b/eddy/feedsRun.EddyHigh_b_Test
index e04dd59ef869ba9c01ec03ee9e79ae97ac14a738..627b423df997d039a4fdb4e03ce91153d9c0a2cd 100755
--- a/eddy/feedsRun.EddyHigh_b_Test
+++ b/eddy/feedsRun.EddyHigh_b_Test
@@ -41,17 +41,19 @@ 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=${indir}/EddyHigh_b_TestData/eddyData/testTopup           
+eddy_args="--imain=${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} ${eddy_args} | tail -n1)
+${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} > ${odir}/EddyHigh_b_Test.runEddy.o$$
+output_prefixes=$(tail -n1 ${odir}/EddyHigh_b_Test.runEddy.o$$)
+
 
 # Define some constants
 max_mean_ima_diff=15.0
@@ -65,7 +67,7 @@ for prefix in ${output_prefixes}; do
   else
     precomputed="${indir}/EddyHigh_b_TestData/eddyData/Precomputed/eddy_openmp_output"
   fi
-  
+
   ${thisdir}/EddyHigh_b_Feeds.py ${odir} `basename ${prefix}`            \
       `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/testMask` \
       `imglob -extension ${prefix}`                                      \
diff --git a/eddy/feedsRun.EddyLSRTest b/eddy/feedsRun.EddyLSRTest
index 0e0fdaadf8a3e6ab039c4b8d4e6841087165db89..fd8212f708b630c4dabb4e18c2496b0069071838 100755
--- a/eddy/feedsRun.EddyLSRTest
+++ b/eddy/feedsRun.EddyLSRTest
@@ -38,18 +38,20 @@ if [ ! -d "$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=${indir}/EddyLSRTestData/eddyData/testTopup        
-           --resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 
+eddy_args="--imain=${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} ${eddy_args} | tail -n1)
+${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} > ${odir}/EddyLSRTest.runEddy.o$$
+output_prefixes=$(tail -n1 ${odir}/EddyLSRTest.runEddy.o$$)
+
 
 # Define some constants
 max_mean_ima_diff=15.0
diff --git a/eddy/feedsRun.EddyMBSTest b/eddy/feedsRun.EddyMBSTest
index 273f2adf8c79cd393bbcef64caccc82c03cf597b..488fdf85b6c4ae9b7e51fd0f04eff4c29ed3470e 100755
--- a/eddy/feedsRun.EddyMBSTest
+++ b/eddy/feedsRun.EddyMBSTest
@@ -43,19 +43,20 @@ 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=${indir}/EddyMBSTestData/eddyData/testTopup           
-           --fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000               
-           --flm=quadratic --dont_peas --estimate_move_by_susceptibility 
+eddy_args="--imain=${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} ${eddy_args} | tail -n1)
+${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} > ${odir}/EddyMBSTest.runEddy.o$$
+output_prefixes=$(tail -n1 ${odir}/EddyMBSTest.runEddy.o$$)
 
 # Define some constants
 max_mean_dfield_diff=0.03
@@ -66,7 +67,7 @@ max_max_ima_diff=0.6
 
 # Check the results against precomputed results
 
-for prefix in ${output_prefixes}; do    
+for prefix in ${output_prefixes}; do
     ${thisdir}/MoveBySuscFeeds.py ${odir} `basename ${prefix}`                                                           \
         `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/BrainMaskForComparison`                         \
         `imglob -extension ${prefix}`                                                                                    \
diff --git a/eddy/feedsRun.EddyS2VTest b/eddy/feedsRun.EddyS2VTest
index c2ae8867bc510ab5125f8d4f26b3518347424656..6d79f0df2b4806d768292c4db44159f287b2896f 100755
--- a/eddy/feedsRun.EddyS2VTest
+++ b/eddy/feedsRun.EddyS2VTest
@@ -40,20 +40,21 @@ if [ ! -d "$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                          
+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} ${eddy_args} | tail -n1)
+${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} > ${odir}/EddyS2VTest.runEddy.o$$
+output_prefixes=$(tail -n1 ${odir}/EddyS2VTest.runEddy.o$$)
 
 # Define some constants
 # These are for the comparison of output images divided on b=0, b=700 and b=2000
diff --git a/eddy/feedsRun.EddyTest b/eddy/feedsRun.EddyTest
index 3c0d2b23e23944fa69af129cbe4454a5d4ba8559..6edd25f6e48e6f9d4183775aa086eaf077df1b57 100755
--- a/eddy/feedsRun.EddyTest
+++ b/eddy/feedsRun.EddyTest
@@ -37,16 +37,17 @@ 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 
+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} ${eddy_args} | tail -n1)
+${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} > ${odir}/EddyTest.runEddy.o$$
+output_prefixes=$(tail -n1 ${odir}/EddyTest.runEddy.o$$)
 
 # Define some constants
 max_mean_dfield_diff=0.5
diff --git a/eddy/runEddy b/eddy/runEddy
index 3dba71df787ea5dcfe5d395e3c7aa5ed10cf48ec..8e583c1fcb09c3ac9ff06c6166fd0b95cfac3877 100755
--- a/eddy/runEddy
+++ b/eddy/runEddy
@@ -67,10 +67,14 @@ do
     fsl_sub="fsl_sub -l ${outdir} -q long.q -s openmp,6"
   fi
 
-  jid=`${fsl_sub} ${exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
-  if [ $? -ne 0 ]; then
-    echo "Error submitting ${exe} ${eddy_args}"
-    exit 1
+  # fsl_sub will return an error (and not
+  # output a job id) if we try to run a
+  # cuda exe on a non-cuda-capable machine
+  # or queue. So we allow it to fail.
+  jid=$(${fsl_sub} ${exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args} || true)
+  if [ "${jid}" == "" ]; then
+    echo "Error submitting ${exe} - skipping"
+    continue
   fi
 
   if [[ "${exe}" == *"cuda"* ]]; then
@@ -80,6 +84,11 @@ do
   fi
 done
 
+if [ "${cuda_jids}" == "" ] && [ "${cpu_jids}" == "" ]; then
+  echo "Unable to submit any eddy executables!"
+  exit 1
+fi
+
 # If running on a cluster, wait
 # until all jobs have finished.
 # If not running on a cluster,