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Major re-arrangement of eddy tests

Merged Paul McCarthy requested to merge rf/eddy into master
Files
6
@@ -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)
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