Bf/set sge

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}`                                      \