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add compatibility to old version
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Not needed for now, just future-proofing
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@hcmh
hcmh committed Jan 24, 2022
1 parent 5d90205 commit 64f4589
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Showing 29 changed files with 65 additions and 35 deletions.
3 changes: 2 additions & 1 deletion Figure10/Fig10.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=../brain
dir1=..
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3 changes: 2 additions & 1 deletion Figure2/Fig2.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

#---------------- Figure 2A -----------------------------
dir=../phantom
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3 changes: 2 additions & 1 deletion Figure3/Fig3.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=../brain
dir1=..
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5 changes: 3 additions & 2 deletions Figure6/Fig6.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=../liver
dir1=..
Expand Down Expand Up @@ -79,4 +80,4 @@ done
bart join 0 `seq -f "tmp_mean_ROI%g" $beg $end` mean_ROIs

rm tmp*
rm T1map*
rm T1map*
5 changes: 3 additions & 2 deletions Figure7/Fig7A.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

# Show all SMS 5 results
dir=../brain
Expand Down Expand Up @@ -66,4 +67,4 @@ bart join 0 `seq -f "tmp_t1map_masked_%g" $beg $end` T1map_ssl_masked
bart join 1 T1map_masked_joint T1map_ssl_masked Fig07A

rm tmp*
rm T1map*
rm T1map*
5 changes: 3 additions & 2 deletions Figure7/Fig7B.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=../liver
dir1=..
Expand Down Expand Up @@ -64,4 +65,4 @@ bart resize -c 1 180 tmp_t1map_masked_joint_1 T1map-ssl_masked_joint
bart join 1 T1map_masked_joint T1map-ssl_masked_joint Fig07B

rm tmp*
rm T1map*
rm T1map*
3 changes: 2 additions & 1 deletion Figures_4_and_5/Fig4A.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

#---------------- Figure 4A -----------------------------
dir=../brain
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3 changes: 2 additions & 1 deletion Figures_4_and_5/Fig4B.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

#---------------- Figure 4B -----------------------------
dir=../brain
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3 changes: 2 additions & 1 deletion VideoS1/Supp_V1.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=../brain
dir1=..
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3 changes: 2 additions & 1 deletion VideoS2/Supp_V2.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=../brain
dir1=..
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3 changes: 2 additions & 1 deletion VideoS3/Supp_V3.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=../liver
dir1=..
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3 changes: 2 additions & 1 deletion all.sh
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Expand Up @@ -14,12 +14,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

# phantom
./run_ss_phantom.sh
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3 changes: 2 additions & 1 deletion post.sh
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Expand Up @@ -52,12 +52,13 @@ if [ ! -e $reco ] ; then
exit 1
fi

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"


#WORKDIR=$(mktemp -d)
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3 changes: 2 additions & 1 deletion prep.sh
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Expand Up @@ -13,12 +13,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

helpstr=$(cat <<- EOF
Preparation of traj, data and inversion times for IR SMS Radial FLASH.
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3 changes: 2 additions & 1 deletion reco.sh
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Expand Up @@ -78,12 +78,13 @@ if [ ! -e $ksp ] ; then
exit 1
fi

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"


#WORKDIR=$(mktemp -d)
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3 changes: 2 additions & 1 deletion run_inter3_brain.sh
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Expand Up @@ -13,12 +13,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=brain/inter3

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5 changes: 3 additions & 2 deletions run_inter3_liver.sh
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Expand Up @@ -13,12 +13,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=liver/inter3
dir2=liver/sms3
Expand Down Expand Up @@ -46,4 +47,4 @@ bart scale 1. $dir/$prefix data/_ksp
./prep.sh -s$sample -R$TR -G$GA -p$nspokes -f$nspokes_per_frame -m$sms -S$slices -c$nstate data/_ksp $dir2/coil_index/vol_1.txt ${prefix}-data.coo ${prefix}-traj.coo ${prefix}-TI.coo
./reco.sh -m$sms -R$lambda -k -o$overgrid ${prefix}-TI.coo ${prefix}-traj.coo ${prefix}-data.coo ${prefix}-liver-reco-${reg}.coo | tee -a $prefix.log
./post.sh -R$TR -r$res ${prefix}-liver-reco-${reg}.coo ${prefix}-liver-${reg}-t1map.coo
rm ${prefix}-traj.coo ${prefix}-data.coo
rm ${prefix}-traj.coo ${prefix}-data.coo
3 changes: 2 additions & 1 deletion run_inter5_brain.sh
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Expand Up @@ -13,12 +13,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=brain/inter5

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3 changes: 2 additions & 1 deletion run_sms3_brain.sh
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Expand Up @@ -13,12 +13,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

if [ $# -eq 0 ]; then
vols=1
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3 changes: 2 additions & 1 deletion run_sms3_gaal_brain.sh
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Expand Up @@ -13,12 +13,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=brain/sms3-aligned

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6 changes: 3 additions & 3 deletions run_sms3_gaal_liver.sh
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Expand Up @@ -13,12 +13,12 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

dir=liver/sms3-aligned
dir2=liver/sms3
Expand Down Expand Up @@ -46,4 +46,4 @@ bart scale 1. $dir/$prefix data/_ksp
./prep.sh -s$sample -R$TR -G$GA -p$nspokes -f$nspokes_per_frame -m$sms -S$slices -c$nstate data/_ksp $dir2/coil_index/vol_1.txt ${prefix}-data.coo ${prefix}-traj.coo ${prefix}-TI.coo
./reco.sh -m$sms -R$lambda -k -o$overgrid ${prefix}-TI.coo ${prefix}-traj.coo ${prefix}-data.coo ${prefix}-liver-reco-${reg}.coo | tee -a $prefix.log
./post.sh -R$TR -r$res ${prefix}-liver-reco-${reg}.coo ${prefix}-liver-${reg}-t1map.coo
rm ${prefix}-traj.coo ${prefix}-data.coo
rm ${prefix}-traj.coo ${prefix}-data.coo
3 changes: 2 additions & 1 deletion run_sms3_liver.sh
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Expand Up @@ -13,12 +13,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

if [ $# -eq 0 ]; then
vols=1
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4 changes: 3 additions & 1 deletion run_sms3_phantom.sh
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Expand Up @@ -13,12 +13,14 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"


dir=phantom

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3 changes: 2 additions & 1 deletion run_sms5_brain.sh
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Expand Up @@ -13,12 +13,13 @@

set -e

export PATH=$TOOLBOX_PATH:$PATH

if [ ! -e $TOOLBOX_PATH/bart ] ; then
echo "\$TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
export PATH=$TOOLBOX_PATH:$PATH
export BART_COMPAT_VERSION="v0.7.00"

if [ $# -eq 0 ]; then
vols=1
Expand Down
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