1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
|
#!/bin/bash
# Copyright 2022. TU Graz. Institute of Biomedical Imaging.
# Author: Moritz Blumenthal
#
# F. Ong, M. Uecker and M. Lustig, Accelerating Non-Cartesian
# MRI Reconstruction Convergence Using k-Space Preconditioning
# IEEE TMI, 2020 39:1646-1654
#
helpstr=$(cat <<- EOF
Compute k-space preconditioner P such that ||P^2 AA^H - 1|| is minimal
Note the square in the definition. The preconditioner can be used directly as wights in PICS.
<ones> contains ones with image dimensions
-B file subspace basis
-g use GPU
-h help
EOF
)
usage="Usage: $0 [-h] [-g] [-B <basis>] <ones> <trajectory> <output>"
GPU=""
BASIS=""
while getopts "hgB:" opt; do
case $opt in
g)
GPU="-g"
;;
B)
BASIS=$(readlink -f "$OPTARG")
;;
h)
echo "$usage"
echo
echo "$helpstr"
exit 0
;;
\?)
echo "$usage" >&2
exit 1
;;
esac
done
shift $((OPTIND - 1))
if [ $# -lt 3 ] ; then
echo "$usage" >&2
exit 1
fi
if [ ! -e "$BART_TOOLBOX_PATH"/bart ] ; then
if [ -e "$TOOLBOX_PATH"/bart ] ; then
BART_TOOLBOX_PATH="$TOOLBOX_PATH"
else
echo "\$BART_TOOLBOX_PATH is not set correctly!" >&2
exit 1
fi
fi
export PATH="$BART_TOOLBOX_PATH:$PATH"
ones=$(readlink -f "$1")
traj=$(readlink -f "$2")
prec=$(readlink -f "$3")
WORKDIR=`mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir'`
trap 'rm -rf "$WORKDIR"' EXIT
cd $WORKDIR
X=$(bart show -d0 $ones)
Y=$(bart show -d1 $ones)
Z=$(bart show -d2 $ones)
s1=$((X*Y*Z))
if [[ 1 != $X ]] ; then X=$((2*X)); fi
if [[ 1 != $Y ]] ; then Y=$((2*Y)); fi
if [[ 1 != $Z ]] ; then Z=$((2*Z)); fi
s2=$((X*Y*Z))
s3=$(echo "$s1*e(-1.5*l($s2))"|bc -l)
bart fmac -C -s7 $ones $ones mps_norm2
bart scale $s3 mps_norm2 scale
ksp_dims="1"
for i in $(seq 15); do
ksp_dims+=" $(bart show -d$i $traj)"
done
if [[ "$BASIS" != "" ]] ; then
bart fmac -C -s$(bart bitmask 6) $BASIS $BASIS bas_scale
bart fmac scale bas_scale scale2
bart copy scale2 scale
COE=$(bart show -d6 $BASIS)
bart transpose 6 7 $BASIS basis_r
bart fmac -C $BASIS basis_r basis_2
bart reshape $(bart bitmask 6 7) $((COE*COE)) 1 basis_2 basis
BASIS="-B basis"
fi
bart ones 16 $ksp_dims ksp
bart scale 2 $traj traj2
bart nufft $BASIS -P --lowmem --no-precomp -a $GPU -x$X:$Y:$Z traj2 ksp psf
bart resize -c 0 $X 1 $Y 2 $Z $ones ones_os
bart fft -u 7 ones_os ones_ksp1
bart fmac -C ones_ksp1 ones_ksp1 ones_ksp
bart fft -u -i 7 ones_ksp ones_img
bart fmac psf ones_img psf_mul
bart nufft $BASIS -P --lowmem --no-precomp $GPU traj2 psf_mul pre_inv
bart creal pre_inv pre_inv_real
bart invert pre_inv_real pre_real
bart fmac pre_real scale pre_sqr
bart spow -- 0.5 pre_sqr $prec
|
