-
Notifications
You must be signed in to change notification settings - Fork 3
/
dcm_coreg.bash
executable file
·412 lines (345 loc) · 14.2 KB
/
dcm_coreg.bash
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
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
#!/bin/bash
#
# dcm_coreg.bash
#
# Copyright 2008 Rudolph Pienaar
# Massachusetts General Hospital
#
# GPL v2
#
# "include" the set of common script functions
source common.bash
declare -i Gi_verbose=0
declare -i Gb_useExpertOptions=0
declare -i Gb_useOverrideOut=0
declare -i Gb_forceStage=1
declare -i Gb_useMatrix=0
G_LOGDIR="-x"
G_OUTDIR="/chb/users/dicom/postproc"
G_OUTRUNDIR="-x"
G_OUTPREFIX="-x"
G_DICOMINPUTDIR="-x"
G_DICOMINPUTFILE="-x"
G_DICOMINPUTREF="-x"
G_INPUTMAT="-x"
G_FLIRTOPT="-x"
G_STAGES="12"
G_SYNOPSIS="
NAME
dcm_coreg.bash
SYNOPSIS
dcm_coreg.bash -D <dicomInputDir> \\
-d <dicomInputFile> \\
-r <dicomInputReferenceFile> \\
-o <outputRunDir> \\
[-E] \\
[-m <inputMatrix>] \\
[-v <verbosity>] \\
[-O <experimentTopDir>] \\
[-p <outputPrefix>]
DESCRIPTION
'dcm_coreg.bash' is a thin wrapper about a 'flirt' registration
process that co-registers an input volume to a reference volume.
These volumes are specified as DICOM format files.
The script (after checking for some simple failure conditions)
converts the relevant volumes to analyze format, and then calls
'flirt'. Additional options to 'flirt' can be specified in the
<flirtOptsFile>, whose contents are blindly appended to the
'flirt' command line.
If 4D input volumes are detected, the script will automatically
run a second-pass of 'flirt' to apply the registration to each
underlying volume component.
ARGUMENTS
-v <level> (optional)
Verbosity level.
-D <dicomInputDir>
The directory containing DICOM files for a particular study.
-d <dicomInputFile>
A file in <dicomInputDir> specifying the volume to use as 'input'
for registration. All files in this series are automatically
converted to a single Analyze format volume.
-r <dicomInputReferenceFile>
A file in <dicomInputDir> specifying the volume to use as 'reference'
for registration. All files in this series are automatically
converted to a single Analyze format volume.
-O <experimentTopDir> (optional) (Default: $G_OUTDIR)
The root directory node that contains the outputs of a particular
registration run. Each run is stored in its own directory.
-o <outputRunDir>
A descriptive name prefixed to each volume generated by a registration
run.
-E (Optional)
Use 'expert' option files. For each processing run, if this flag
is indicated, the output directory will be scanned for any files
named <STAGEPROC>.opt -- which if found will be parsed and their
contents appended *blindly* to the <STAGECMD> for that stage.
-p <outputPrefix> (Optional)
If specified, prefix all generated output files with <outputPrefix>.
PRECONDITIONS
o nde
POSTCONDITIONS
o Output registered volumes (and matrices) are stored in:
<experimentTopDir>/<outputRunDir>
with the output volume and output matrix files:
<outputPrefix>-registered.[{img}{mat}]
HISTORY
12 September 2008
o Initial design and coding.
15 August 2011
o Added 4D volume detection.
EXAMPLE USE:
Assuming you are in currently in a directory and containing the
input DICOMS as flat files, with the first file of the reference
series called <ref>.dcm and the first file of the input series
called <input>.dcm, and assuming you want the output to be in a
new subjectory 'output' and an experiment called 'series',
$>dcm_coreg.bash -v 1 \\
-D $(pwd) \\
-r <ref>.dcm -d <input>.dcm \\
-O output -o series
"
###\\\
# Globals are in capital letters. Immutable globals are prefixed by 'G'.
###///
G_SELF=`basename $0`
G_PID=$$
# Actions
A_fileCheck="checking for a required file dependency"
A_noDicomDir="checking on input DICOM directory"
A_noOutRunDir="checking on output run directory"
A_noDicomFile="checking on input DICOM file"
A_noDicomRefFile="checking on input DICOM reference file"
A_noMatrixFile="checking on input matrix reference file"
A_noDicomDirArg="checking on -d <dicomInputDir> argument"
A_noExpDir="checking on the output root directory"
A_metaLog="checking the meta log file"
A_runflirt="executing 'flirt'"
A_noFlirt="checking for the 'flirt' binary"
A_exitFlirt="running the 'flirt' process"
A_dependencyStage="checking for a required dependency from an earlier stage"
A_stageRun="running a stage in the processing pipeline"
A_dimNumCheck="checking on the number of dimensions of input and ref"
# Error messages
EM_fileCheck="it seems that a dependency is missing."
EM_noDicomDir="I couldn't access the input DICOM dir. Does it exist?"
EM_noOutRunDir="I couldn't access the output run dir. Does it exist?"
EM_noDicomFile="I couldn't find the input DICOM file. Does it exist?"
EM_noDicomRefFile="I couldn't find an input DICOM reference file. Does it exist?"
EM_noMatrixFile="I couldn't find an input matrix reference file. Does it exist?"
EM_noDicomDirArg="it seems as though you didn't specify a -D <dicomInputDir>."
EM_noExpDir="I couldn't find the <expDir>."
EM_metaLog="it seems as though this stage has already run.\n\tYou can force execution with a '-F'"
EM_runflirt="the process died unexpectedly."
EM_noFlirt="I couldn't find 'flirt' anywhere on your path."
EM_exitFlirt="it seems as though an unexpected exit has occurred."
EM_dependencyStage="it seems that a stage dependency is missing."
EM_stageRun="I encountered an error processing this stage."
EM_dimNumCheck="number of dimensions are inconsistent."
# Error codes
EC_fileCheck=1
EC_dependencyStage=2
EC_stageRun=30
EC_noDicomDir=50
EC_noOutRunDir=54
EC_noDicomDirArg=51
EC_noDicomFile=52
EC_noDicomRefFile=53
EC_noMatrixFile=54
EC_noExpDir=23
EC_metaLog=80
EC_runflirt=90
EC_noFlirt=40
EC_exitFlirt=41
EC_dimNumCheck=50
# Defaults
D_whatever=
###\\\
# Function definitions
###///
###\\\
# Process command options
###///
while getopts D:d:v:E:m:o:r:O:p: option ; do
case "$option"
in
D) G_DICOMINPUTDIR=$OPTARG ;;
d) Gb_useDICOMFile=1
G_DICOMINPUTFILE=$OPTARG ;;
v) let Gi_verbose=$OPTARG ;;
E) Gb_useExpertOptions=1 ;;
m) G_INPUTMAT=$OPTARG
Gb_useMatrix=1 ;;
O) G_OUTDIR=$OPTARG ;;
r) G_DICOMINPUTREF=$OPTARG ;;
o) Gb_useOverrideOut=1
G_OUTRUNDIR="$OPTARG" ;;
p) G_OUTPREFIX="$OPTARG" ;;
\?) synopsis_show
exit 0;;
esac
done
verbosity_check
topDir=$(pwd)
cprint "hostname" "[ $(hostname) ]"
## Check on script preconditions
REQUIREDFILES="common.bash flirt mri_convert dcm_mkIndx.bash"
for file in $REQUIREDFILES ; do
printf "%40s" "Checking for $file"
file_checkOnPath $file || fatal fileCheck
done
## Check on input directory and files
statusPrint "Checking -D <dicomInputDir>"
if [[ "$G_DICOMINPUTDIR" == "-x" ]] ; then fatal noDicomDirArg ; fi
ret_check $?
statusPrint "Checking on <dicomInputDir>"
dirExist_check $G_DICOMINPUTDIR || fatal noDicomDir
cd $G_DICOMINPUTDIR >/dev/null
G_DICOMINPUTDIR=$(pwd)
cd $topDir
cd ${G_DICOMINPUTDIR}
statusPrint "Scanning <dicomInputDir>"
ret_check $?
SCANTABLE=$(dcm_mkIndx.bash -t '_' |tr '(' '_' | tr ')' '_')
statusPrint "Checking input volume"
DICOMINPUT=${G_DICOMINPUTDIR}/${G_DICOMINPUTFILE}
fileExist_check $DICOMINPUT || fatal noDicomFile
INPUTSCAN=$(echo "$SCANTABLE" | grep $G_DICOMINPUTFILE | awk '{print $3}')
cprint "Input scan" "[ $INPUTSCAN ]"
statusPrint "Checking reference volume"
DICOMREFFILE=${G_DICOMINPUTDIR}/${G_DICOMINPUTREF}
fileExist_check $DICOMREFFILE || fatal noDicomRefFile
REFSCAN=$(echo "$SCANTABLE" | grep $G_DICOMINPUTREF | awk '{print $3}')
cprint "Reference scan" "[ $REFSCAN ]"
if [[ $G_OUTPREFIX == "-x" ]] ; then
G_OUTPREFIX="$INPUTSCAN-To-$REFSCAN"
fi
statusPrint "Checking on <outputRunDir>"
if (( !Gb_useOverrideOut )) ; then
MRID=$(echo "$SCANTABLE" | cd | awk '{print $3}')
G_OUTRUNDIR=${MRID}-$G_OUTPREFIX
fi
dirExist_check ${G_OUTDIR}/$G_OUTRUNDIR "not found - creating" \
|| mkdir -p ${G_OUTDIR}/$G_OUTRUNDIR \
|| fatal noOutRunDir
cd ${G_OUTDIR}/$G_OUTRUNDIR >/dev/null
OUTDIR=$(pwd)
cd $topDir
if (( Gb_useMatrix )) ; then
statusPrint "Checking on <inputMatrix> file"
fileExist_check $G_INPUTMAT || fatal noMatrixFile
fi
## Check which stages to process
statusPrint "Checking which stages to process"
barr_stage=([0]=0 [1]=0 [2]=0 [3]=0 [4]=0 [5]=0)
for i in $(seq 1 2) ; do
b_test=$(expr index $G_STAGES "$i")
if (( b_test )) ; then b_flag="1" ; else b_flag="0" ; fi
barr_stage[$i]=$b_flag
done
ret_check $?
G_LOGDIR=$OUTDIR
STAMPLOG=${G_LOGDIR}/${G_SELF}.log
stage_stamp "Init | ($(pwd)) $G_SELF $*" $STAMPLOG
STAGENUM=1
STAGEPROC="mri_convert"
NIFTIIN="${OUTDIR}/${G_OUTPREFIX}-input.nii"
NIFTIREF="${OUTDIR}/${G_OUTPREFIX}-ref.nii"
if (( ${barr_stage[1]} )) ; then
statusPrint \
"$(date) | Processing STAGE 1 - Converting to NIFTI... | START" "\n"
STAGE=${STAGENUM}-${STAGEPROC}
statusPrint "Converting input volume" "\n"
STAGECMD="$STAGEPROC \
$DICOMINPUT \
$NIFTIIN"
stage_run "$STAGE" "$STAGECMD" \
"${OUTDIR}/${STAGEPROC}.std" \
"${OUTDIR}/${STAGEPROC}.err" \
"SILENT" \
|| fatal stageRun
statusPrint "Converting reference volume" "\n"
STAGECMD="$STAGEPROC \
$DICOMREFFILE \
$NIFTIREF"
stage_run "$STAGE" "$STAGECMD" \
"${OUTDIR}/${STAGEPROC}.std" \
"${OUTDIR}/${STAGEPROC}.err" \
"SILENT" \
|| fatal stageRun
statusPrint \
"$(date) | Processing STAGE 1 - Converting to NIFTI... | END" "\n"
fi
STAGE1OUT=$NIFTIIN
STAGE2IN=$STAGE1OUT
STAGENUM=2
STAGEPROC=flirt
STAGE=2-$STAGE2PROC
STAGE2OUTBASE="${G_OUTDIR}/${G_OUTRUNDIR}/${G_OUTPREFIX}-registered"
if (( ${barr_stage[2]} )) ; then
statusPrint "$(date) | Processing STAGE 2 - coregistration | START" "\n"
statusPrint "Checking previous stage dependencies"
fileExist_check $NIFTIIN || fatal dependencyStage
fileExist_check $NIFTIREF || fatal dependencyStage
INMATRIX=""
OUTMATRIX="-omat $STAGE2OUTBASE.mat"
if (( Gb_useMatrix )) ; then
MATRIX="-applyxfm -init $G_INPUTMAT"
OUTMATRIX=""
fi
EXOPTS=$(eval expertOpts_parse $STAGEPROC)
STAGE=${STAGENUM}-${STAGEPROC}
STAGECMD="$STAGEPROC \
-dof 6 \
-cost mutualinfo \
-usesqform \
-in $NIFTIIN \
-ref $NIFTIREF \
-out $STAGE2OUTBASE.nii \
$INMATRIX \
$OUTMATRIX \
$EXOPTS"
stage_run "$STAGE" "$STAGECMD" \
"${OUTDIR}/${STAGEPROC}.std" \
"${OUTDIR}/${STAGEPROC}.err" \
"SILENT" \
|| fatal stageRun
statusPrint "$(date) | Processing STAGE 2 - coregistration | END" "\n"
fi
#
# If the inputs are 4D, need to apply the transform to each
# underlying volume in the set.
#
dimensionsIn=$(mri_info $NIFTIIN | grep dimensions |\
awk -F \: '{print $2}' | awk -F x '{print NF}')
dimensionsRef=$(mri_info $NIFTIREF | grep dimensions |\
awk -F \: '{print $2}' | awk -F x '{print NF}')
if (( dimensionsRef != dimensionsIn )) ; then fatal dimNumCheck ; fi
STAGENUM=3
STAGEPROC=flirt
STAGE=3-$STAGE2PROC
STAGE3OUTBASE="${G_OUTDIR}/${G_OUTRUNDIR}/${G_OUTPREFIX}-registered4D"
if (( dimensionsIn == 4 )) ; then
statusPrint "$(date) | Processing STAGE 3 (extra) - 4D volume registration | START" "\n"
statusPrint "Input data is 4D... Applying transform to all underlying volumes" "\n"
EXOPTS=$(eval expertOpts_parse $STAGEPROC)
STAGE=${STAGENUM}-${STAGEPROC}
STAGECMD="$STAGEPROC \
-dof 6 \
-cost mutualinfo \
-usesqform \
-in $NIFTIIN \
-ref $NIFTIREF \
-out $STAGE3OUTBASE.nii \
-applyxfm \
-init $STAGE2OUTBASE.mat \
$EXOPTS"
stage_run "$STAGE" "$STAGECMD" \
"${OUTDIR}/${STAGEPROC}.std" \
"${OUTDIR}/${STAGEPROC}.err" \
"SILENT" \
|| fatal stageRun
statusPrint "$(date) | Processing STAGE 3 (extra) - 4D volume registration | END" "\n"
statusPrint "Final output is $STAGE3OUTBASE.nii"
fi
verbosity_check
shut_down 0