From 5bef154ec845235b88b64fcff516e44c31d64f15 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 24 Nov 2021 12:22:46 +0000
Subject: [PATCH] BF: Fix multi-line strings, wrong var name in runEddy
---
eddy/feedsRun.EddyHigh_b_Test | 16 ++++++++--------
eddy/feedsRun.EddyLSRTest | 18 +++++++++---------
eddy/feedsRun.EddyMBSTest | 20 ++++++++++----------
eddy/feedsRun.EddyS2VTest | 22 +++++++++++-----------
eddy/feedsRun.EddyTest | 14 +++++++-------
eddy/runEddy | 6 +++---
6 files changed, 48 insertions(+), 48 deletions(-)
diff --git a/eddy/feedsRun.EddyHigh_b_Test b/eddy/feedsRun.EddyHigh_b_Test
index 7b238aa..e04dd59 100755
--- a/eddy/feedsRun.EddyHigh_b_Test
+++ b/eddy/feedsRun.EddyHigh_b_Test
@@ -41,14 +41,14 @@ 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 " \
- "--nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose"
+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} ${eddy_args} | tail -n1)
diff --git a/eddy/feedsRun.EddyLSRTest b/eddy/feedsRun.EddyLSRTest
index d965a57..0e0fdaa 100755
--- a/eddy/feedsRun.EddyLSRTest
+++ b/eddy/feedsRun.EddyLSRTest
@@ -38,15 +38,15 @@ if [ ! -d "$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=${indir}/EddyLSRTestData/eddyData/testTopup " \
- "--resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 " \
- "--dont_peas --very_verbose"
+eddy_args="--imain=${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} ${eddy_args} | tail -n1)
diff --git a/eddy/feedsRun.EddyMBSTest b/eddy/feedsRun.EddyMBSTest
index babc78e..273f2ad 100755
--- a/eddy/feedsRun.EddyMBSTest
+++ b/eddy/feedsRun.EddyMBSTest
@@ -43,16 +43,16 @@ if [ ! -d "$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=${indir}/EddyMBSTestData/eddyData/testTopup " \
- "--fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000 " \
- "--flm=quadratic --dont_peas --estimate_move_by_susceptibility " \
- "--mbs_niter=20 --mbs_lambda=10 --mbs_ksp=10 --very_verbose"
+eddy_args="--imain=${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} ${eddy_args} | tail -n1)
diff --git a/eddy/feedsRun.EddyS2VTest b/eddy/feedsRun.EddyS2VTest
index a511d5d..c2ae886 100755
--- a/eddy/feedsRun.EddyS2VTest
+++ b/eddy/feedsRun.EddyS2VTest
@@ -40,17 +40,17 @@ if [ ! -d "$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 " \
- "--slspec=${indir}/EddyS2VTestData/eddyData/testSlspec "
+eddy_args="--imain=${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} ${eddy_args} | tail -n1)
diff --git a/eddy/feedsRun.EddyTest b/eddy/feedsRun.EddyTest
index c50ac5e..3c0d2b2 100755
--- a/eddy/feedsRun.EddyTest
+++ b/eddy/feedsRun.EddyTest
@@ -37,13 +37,13 @@ if [ ! -d "$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 " \
- "--repol --fwhm=10,0,0,0,0 --dfields -v"
+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)
diff --git a/eddy/runEddy b/eddy/runEddy
index 10531b4..28f5c37 100755
--- a/eddy/runEddy
+++ b/eddy/runEddy
@@ -57,7 +57,7 @@ for cuda_exe in ${cuda_exes};
do
tmp=`basename ${cuda_exe}`
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}"
done
@@ -66,7 +66,7 @@ for cpu_exe in ${cpu_exes};
do
tmp=`basename ${cuda_exe}`
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}"
done
@@ -108,7 +108,7 @@ for exe in ${cuda_exes} ${cpu_exes};
do
tmp=`basename ${cuda_exe}`
variant=`echo ${tmp} | sed 's/eddy_//'`
- prefix="${odir}/eddyOutput_${variant}"
+ prefix="${outdir}/eddyOutput_${variant}"
outputs="${outputs} ${prefix}"
if [ ! -f ${prefix}.nii* ]; then
echo "${prefix} is missing"
--
GitLab