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run_phantom_single_shot.sh
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#!/bin/bash
#
# Copyright 2022. TU Graz. Institute of Biomedical Imaging.
# Copyright 2022. Uecker Lab. University Medical Center Göttingen.
#
# Author:
# Xiaoqing Wang, 2020-2022
#
# Wang X et al.
# Free-Breathing Myocardial T1 Mapping using Inversion-Recovery
# Radial FLASH and Motion-Resolved Model-Based Reconstruction.
# Magn Reson Med. (2022), DOI: 10.1002/mrm.29521.
set -eux
dir=phantom
[ -d $dir ] || mkdir $dir
cd $dir
infile=../data/phantom/raw_data
delays=($(ls -d $infile/delay*))
nIRs=3
for i in "${delays[@]}"
do
echo "$i"
tnum=$(echo $i| cut -d'/' -f 5)
echo $tnum
bart extract 12 0 $nIRs $i/ksp tmp_ksp0
NSPK=$(bart show -d1 tmp_ksp0)
NFRM=$(bart show -d10 tmp_ksp0)
bart transpose 1 9 tmp_ksp0 tmp_ksp1
FLAG=$(bart bitmask 9 10 12)
bart reshape $FLAG 1 $((NSPK*NFRM*nIRs)) 1 tmp_ksp1 tmp_ksp2
GA=7
overgrid=1.0
nspokes_per_frame=15
alpha_min=0.002
TR=3270
READ=$(bart show -d0 tmp_ksp2)
NBR=$((READ/2))
nspokes=$(bart show -d10 tmp_ksp2)
opts_prep="-s$READ -R$TR -G$GA -p$nspokes -f$nspokes_per_frame"
./../prep_single_shot.sh $opts_prep tmp_ksp2 tmp-data tmp-traj tmp-TI
NF=$(bart show -d5 tmp-TI)
# reco data from the second inversion
start_IR=1
bart extract 5 $((start_IR*NF/3)) $(((start_IR+1)*NF/3)) tmp-traj tmp-traj1
bart extract 5 $((start_IR*NF/3)) $(((start_IR+1)*NF/3)) tmp-data tmp-data1
bart extract 5 0 $((1*NF/3)) tmp-TI tmp-TI1
./../reco_single_shot.sh -a$alpha_min -k -o$overgrid tmp-TI1 tmp-traj1 tmp-data1 ${tnum}-reco_${start_IR}IR
done
rm tmp*