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Paul McCarthy · Paul McCarthy · Paul McCarthy · Paul McCarthy · b05c75a6 · b05c75a6
--- 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}`                                      \

--- 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} | tee ${odir}/EddyLSRTest.runEddy.o$$
+output_prefixes=$(tail -n1 ${odir}/EddyLSRTest.runEddy.o$$)
+

 # Define some constants
 max_mean_ima_diff=15.0

--- 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} | tee ${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}`                                                                                    \

--- 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} | tee ${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

--- 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} | tee ${odir}/EddyTest.runEddy.o$$
+output_prefixes=$(tail -n1 ${odir}/EddyTest.runEddy.o$$)

 # Define some constants
 max_mean_dfield_diff=0.5

--- a/eddy/runEddy
+++ b/eddy/runEddy
@@ -56,23 +56,30 @@ fi
 # can qalter the openmp jobs below
 cuda_jids=""
 cpu_jids=""
+submitted=""
 for exe in ${cuda_exes} ${cpu_exes};
 do
  variant=`basename ${exe}`
  variant=`echo ${variant} | sed 's/eddy_//'`

  if [[ "${exe}" == *"cuda"* ]]; then
-    fsl_sub="fsl_sub -l ${outdir} -q cuda.q"
+    fsl_sub="fsl_sub -l ${outdir} --coprocessor=cuda"
  else
    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

+  submitted="${submitted} ${exe}"
+
  if [[ "${exe}" == *"cuda"* ]]; then
    cuda_jids="${cuda_jids} ${jid}"
  else
@@ -80,6 +87,11 @@ do
  fi
 done

+if [ "${submitted}" == "" ]; 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,
@@ -114,7 +126,7 @@ fi
 # and check that the main output file
 # was created
 outputs=""
-for exe in ${cuda_exes} ${cpu_exes};
+for exe in ${submitted};
 do
  tmp=`basename ${exe}`
  variant=`echo ${tmp} | sed 's/eddy_//'`

--- a/msm/feedsRun
+++ b/msm/feedsRun
-msm --levels=3 --conf=allparameterssulcDRconf_pairwise_lambda0.1 --inmesh=L.CC00066XX09.sphere.ICO6.template-40.RIGID.surf.gii --trans=L.CC00066XX09_AFFINE_TEMPLATEsphere.reg.surf.gii --refmesh=L.CC00070XX05_AFFINE_TEMPLATEsphere.reg.surf.gii  --indata=L.CC00066XX09.sulc.ICO6.template-40.RIGID.shape.gii --refdata=L.CC00070XX05.sulc.ICO6.template-40.RIGID.shape.gii -o FPD3levels -v >& out
\ No newline at end of file
+#!/usr/bin/env bash
+
+msm --levels=3 --conf=allparameterssulcDRconf_pairwise_lambda0.1 --inmesh=L.CC00066XX09.sphere.ICO6.template-40.RIGID.surf.gii --trans=L.CC00066XX09_AFFINE_TEMPLATEsphere.reg.surf.gii --refmesh=L.CC00070XX05_AFFINE_TEMPLATEsphere.reg.surf.gii  --indata=L.CC00066XX09.sulc.ICO6.template-40.RIGID.shape.gii --refdata=L.CC00070XX05.sulc.ICO6.template-40.RIGID.shape.gii -o FPD3levels -v >& out
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