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Commit 5bef154e authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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BF: Fix multi-line strings, wrong var name in runEddy

parent f90d98ef
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1 merge request!37Major re-arrangement of eddy tests
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eddy/feedsRun.EddyHigh_b_Test
+ 8
− 8
View file @ 5bef154e
...@@ -41,14 +41,14 @@ if [ ! -d "$indir" ]; then ...@@ -41,14 +41,14 @@ if [ ! -d "$indir" ]; then
fi fi
# Prepare arguments to pass to eddy # Prepare arguments to pass to eddy
eddy_args="--imain=${indir}/EddyHigh_b_TestData/eddyData/testData " \ eddy_args="--imain=${indir}/EddyHigh_b_TestData/eddyData/testData
"--mask=${indir}/EddyHigh_b_TestData/eddyData/testMask " \ --mask=${indir}/EddyHigh_b_TestData/eddyData/testMask
"--bvals=${indir}/EddyHigh_b_TestData/eddyData/testBvals " \ --bvals=${indir}/EddyHigh_b_TestData/eddyData/testBvals
"--bvecs=${indir}/EddyHigh_b_TestData/eddyData/testBvecs " \ --bvecs=${indir}/EddyHigh_b_TestData/eddyData/testBvecs
"--index=${indir}/EddyHigh_b_TestData/eddyData/testIndex " \ --index=${indir}/EddyHigh_b_TestData/eddyData/testIndex
"--acqp=${indir}/EddyHigh_b_TestData/eddyData/testAcqparams " \ --acqp=${indir}/EddyHigh_b_TestData/eddyData/testAcqparams
"--topup=${indir}/EddyHigh_b_TestData/eddyData/testTopup " \ --topup=${indir}/EddyHigh_b_TestData/eddyData/testTopup
"--nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose" --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose"
# run eddy # run eddy
output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1) output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
......
eddy/feedsRun.EddyLSRTest
+ 9
− 9
View file @ 5bef154e
...@@ -38,15 +38,15 @@ if [ ! -d "$indir" ]; then ...@@ -38,15 +38,15 @@ if [ ! -d "$indir" ]; then
fi fi
# Prepare arguments to pass to eddy # Prepare arguments to pass to eddy
eddy_args="--imain=${indir}/EddyLSRTestData/eddyData/testData " \ eddy_args="--imain=${indir}/EddyLSRTestData/eddyData/testData
"--mask=${indir}/EddyLSRTestData/eddyData/testMask " \ --mask=${indir}/EddyLSRTestData/eddyData/testMask
"--bvals=${indir}/EddyLSRTestData/eddyData/testBvals " \ --bvals=${indir}/EddyLSRTestData/eddyData/testBvals
"--bvecs=${indir}/EddyLSRTestData/eddyData/testBvecs " \ --bvecs=${indir}/EddyLSRTestData/eddyData/testBvecs
"--index=${indir}/EddyLSRTestData/eddyData/testIndex " \ --index=${indir}/EddyLSRTestData/eddyData/testIndex
"--acqp=${indir}/EddyLSRTestData/eddyData/testAcqparams " \ --acqp=${indir}/EddyLSRTestData/eddyData/testAcqparams
"--topup=${indir}/EddyLSRTestData/eddyData/testTopup " \ --topup=${indir}/EddyLSRTestData/eddyData/testTopup
"--resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 " \ --resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0
"--dont_peas --very_verbose" --dont_peas --very_verbose"
# run eddy # run eddy
output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1) output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
......
eddy/feedsRun.EddyMBSTest
+ 10
− 10
View file @ 5bef154e
...@@ -43,16 +43,16 @@ if [ ! -d "$indir" ]; then ...@@ -43,16 +43,16 @@ if [ ! -d "$indir" ]; then
fi fi
# Prepare arguments to pass to eddy # Prepare arguments to pass to eddy
eddy_args="--imain=${indir}/EddyMBSTestData/eddyData/testData " \ eddy_args="--imain=${indir}/EddyMBSTestData/eddyData/testData
"--acqp=${indir}/EddyMBSTestData/eddyData/testAcqparams " \ --acqp=${indir}/EddyMBSTestData/eddyData/testAcqparams
"--mask=${indir}/EddyMBSTestData/eddyData/testMask " \ --mask=${indir}/EddyMBSTestData/eddyData/testMask
"--index=${indir}/EddyMBSTestData/eddyData/testIndex " \ --index=${indir}/EddyMBSTestData/eddyData/testIndex
"--bvecs=${indir}/EddyMBSTestData/eddyData/testBvecs " \ --bvecs=${indir}/EddyMBSTestData/eddyData/testBvecs
"--bvals=${indir}/EddyMBSTestData/eddyData/testBvals " \ --bvals=${indir}/EddyMBSTestData/eddyData/testBvals
"--topup=${indir}/EddyMBSTestData/eddyData/testTopup " \ --topup=${indir}/EddyMBSTestData/eddyData/testTopup
"--fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000 " \ --fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000
"--flm=quadratic --dont_peas --estimate_move_by_susceptibility " \ --flm=quadratic --dont_peas --estimate_move_by_susceptibility
"--mbs_niter=20 --mbs_lambda=10 --mbs_ksp=10 --very_verbose" --mbs_niter=20 --mbs_lambda=10 --mbs_ksp=10 --very_verbose"
# run eddy # run eddy
output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1) output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
......
eddy/feedsRun.EddyS2VTest
+ 11
− 11
View file @ 5bef154e
...@@ -40,17 +40,17 @@ if [ ! -d "$indir" ]; then ...@@ -40,17 +40,17 @@ if [ ! -d "$indir" ]; then
fi fi
# Prepare arguments to pass to eddy # Prepare arguments to pass to eddy
eddy_args="--imain=${indir}/EddyS2VTestData/eddyData/testData " \ eddy_args="--imain=${indir}/EddyS2VTestData/eddyData/testData
"--mask=${indir}/EddyS2VTestData/eddyData/testMask " \ --mask=${indir}/EddyS2VTestData/eddyData/testMask
"--bvals=${indir}/EddyS2VTestData/eddyData/testBvals " \ --bvals=${indir}/EddyS2VTestData/eddyData/testBvals
"--bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs " \ --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs
"--index=${indir}/EddyS2VTestData/eddyData/testIndex " \ --index=${indir}/EddyS2VTestData/eddyData/testIndex
"--acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams " \ --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams
"--repol --ol_type=slice --ol_nstd=6 --ol_nvox=500 " \ --repol --ol_type=slice --ol_nstd=6 --ol_nvox=500
"--niter=8 --fwhm=10,6,4,2,0,0,0,0 --nvoxhp=5000 " \ --niter=8 --fwhm=10,6,4,2,0,0,0,0 --nvoxhp=5000
"--mporder=16 --s2v_niter=10 --s2v_interp=trilinear " \ --mporder=16 --s2v_niter=10 --s2v_interp=trilinear
"--s2v_lambda=1 --very_verbose " \ --s2v_lambda=1 --very_verbose
"--slspec=${indir}/EddyS2VTestData/eddyData/testSlspec " --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec "
# run eddy # run eddy
output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1) output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
......
eddy/feedsRun.EddyTest
+ 7
− 7
View file @ 5bef154e
...@@ -37,13 +37,13 @@ if [ ! -d "$indir" ]; then ...@@ -37,13 +37,13 @@ if [ ! -d "$indir" ]; then
fi fi
# Prepare arguments to pass to eddy # Prepare arguments to pass to eddy
eddy_args="--imain=${indir}/EddyTestData/eddyData/testData " \ eddy_args="--imain=${indir}/EddyTestData/eddyData/testData
"--mask=${indir}/EddyTestData/eddyData/testMask " \ --mask=${indir}/EddyTestData/eddyData/testMask
"--bvals=${indir}/EddyTestData/eddyData/testBvals " \ --bvals=${indir}/EddyTestData/eddyData/testBvals
"--bvecs=${indir}/EddyTestData/eddyData/testBvecs " \ --bvecs=${indir}/EddyTestData/eddyData/testBvecs
"--index=${indir}/EddyTestData/eddyData/testIndex " \ --index=${indir}/EddyTestData/eddyData/testIndex
"--acqp=${indir}/EddyTestData/eddyData/testAcqparams " \ --acqp=${indir}/EddyTestData/eddyData/testAcqparams
"--repol --fwhm=10,0,0,0,0 --dfields -v" --repol --fwhm=10,0,0,0,0 --dfields -v"
# run eddy # run eddy
output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1) output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
......
eddy/runEddy
+ 3
− 3
View file @ 5bef154e
...@@ -57,7 +57,7 @@ for cuda_exe in ${cuda_exes}; ...@@ -57,7 +57,7 @@ for cuda_exe in ${cuda_exes};
do do
tmp=`basename ${cuda_exe}` tmp=`basename ${cuda_exe}`
variant=`echo ${tmp} | sed 's/eddy_//'` 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} ${jid}" cuda_jids="${cuda_jids} ${jid}"
done done
...@@ -66,7 +66,7 @@ for cpu_exe in ${cpu_exes}; ...@@ -66,7 +66,7 @@ for cpu_exe in ${cpu_exes};
do do
tmp=`basename ${cuda_exe}` tmp=`basename ${cuda_exe}`
variant=`echo ${tmp} | sed 's/eddy_//'` 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} ${jid}" cpu_jids="${cpu_jids} ${jid}"
done done
...@@ -108,7 +108,7 @@ for exe in ${cuda_exes} ${cpu_exes}; ...@@ -108,7 +108,7 @@ for exe in ${cuda_exes} ${cpu_exes};
do do
tmp=`basename ${cuda_exe}` tmp=`basename ${cuda_exe}`
variant=`echo ${tmp} | sed 's/eddy_//'` variant=`echo ${tmp} | sed 's/eddy_//'`
prefix="${odir}/eddyOutput_${variant}" prefix="${outdir}/eddyOutput_${variant}"
outputs="${outputs} ${prefix}" outputs="${outputs} ${prefix}"
if [ ! -f ${prefix}.nii* ]; then if [ ! -f ${prefix}.nii* ]; then
echo "${prefix} is missing" echo "${prefix} is missing"
......
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