-
Notifications
You must be signed in to change notification settings - Fork 3
/
fix-diffusion.sh
executable file
·90 lines (77 loc) · 4.69 KB
/
fix-diffusion.sh
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
#!/usr/bin/env bash
## Fixes bug in the MR Diffusion macro from dcmulti's conversion
# of 2D slices to enhanced MR format
#
# - Michael Eager (michael.eager@monash.edu)
# - Monash Biomedical Imaging
#
# Copyright (C) 2014 Michael Eager (michael.eager@monash.edu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Check DCMTK on MASSIVE or Agilent console
if test "${MASSIVEUSERNAME+defined}"; then
if [ ! -x "$(which dcmodify)" ];then
module load dcmtk
fi
else
DCMTK="/home/vnmr1/src/dcmtk-3.6.0/bin"
export PATH="${PATH}":"${DCMTK}"
fi
if [ ! -x "$(which dcmodify)" ];then
error_exit "dcmodify not found (fix-dicoms.sh)"
exit 1
fi
output_dir=$1
MODIFY=1
## COMMON FIXES to enhanced DICOMs
DCMODIFY="dcmodify --no-backup " # --ignore-errors"
files=$(find "${output_dir}" -type f -name "*.dcm" -print0 | grep -v tmp)
# nbdirs=$(ls -1 "${output_dir}"/tmp/slice* | sed 's/.*image0\(.*\)echo.*/\1/' | tail -1)
nbdirs=$(find "${output_dir}/tmp" -name '*slice*.dcm' -print0 | sed 's/.*image0\(.*\)echo.*/\1/' | tail -1)
for idx in $(seq 1 "${nbdirs}"); do
# Grab parameters from first slice in image
dcmdump "${output_dir}/tmp/slice001image$(printf '%03d' ${idx})echo001.dcm" 2>&1 | grep 'Diff' |grep -v Sequence| awk '{print $3}' | tr -d '[]' > "${output_dir}"/diffusion.tmp
# dcmdump output_data/hearttissue.dcm/tmp/slice001image002echo001.dcm 2>&1 | grep Diff | awk '{print $1,$3,$NF}'
if [ -f "${output_dir}"/diffusion.tmp ]; then
declare -a DiffusionSequence
let i=0;while IFS=$'\r\n' read -r line_data; do
DiffusionSequence[i]="${line_data}"; ((++i));
done < "${output_dir}"/diffusion.tmp
echo "Diffusion sequence params: ", "${DiffusionSequence[*]}"
if [ ${#DiffusionSequence[*]} -lt 10 ]; then ## BVal index differs -o ${DiffusionSequence[2]} -lt 10
## (Shared sequence)[0].(MR Diffusion Sequence)[0]
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9075)=NONE" "${output_dir}/$(printf '%04d' ${idx}).dcm"
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9087)=0" "${output_dir}/$(printf '%04d' ${idx}).dcm"
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9147)=${DiffusionSequence[2]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
else
## (Shared sequence)[0].(MR Diffusion Sequence)[0](Directionality)
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9075)=${DiffusionSequence[0]}" "${output_dir}/$(printf '%04d' ${idx}).dcm" ##
## (Shared sequence)[0].(MR Diffusion Sequence)[0](Diff Gradient Orientation)
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9076)[0].(0018,9089)=${DiffusionSequence[1]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
## (Shared sequence)[0].(MR Diffusion Sequence)[0](BValue)
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9087)=${DiffusionSequence[2]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
## (Shared sequence)[0].(MR Diffusion Sequence)[0](Anisotrophy)
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9147)=${DiffusionSequence[3]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
## (Shared sequence)(MR Diffusion Sequence)(B MATRIX sequence)( B val re[XYZ][XYZ])
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9076)[0].(0018,9601)[0].(0018,9602)=${DiffusionSequence[4]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9076)[0].(0018,9601)[0].(0018,9603)=${DiffusionSequence[5]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9076)[0].(0018,9601)[0].(0018,9604)=${DiffusionSequence[6]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9076)[0].(0018,9601)[0].(0018,9605)=${DiffusionSequence[7]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9076)[0].(0018,9601)[0].(0018,9606)=${DiffusionSequence[8]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
${DCMODIFY} -i "(5200,9229)[0].(0018,9117)[0].(0018,9076)[0].(0018,9601)[0].(0018,9607)=${DiffusionSequence[9]}" "${output_dir}/$(printf '%04d' ${idx}).dcm"
fi
fi
done
rm -f "${output_dir}"/diffusion.tmp
# done