forked from liangfu/bet2
-
Notifications
You must be signed in to change notification settings - Fork 0
/
bet
executable file
·402 lines (336 loc) · 13.4 KB
/
bet
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
#!/bin/sh
# bet - wrapper script for lots of different bet functionality
#
# Stephen Smith, FMRIB Image Analysis Group
# SIENA eye cleanup option by Marco Battaglini and Nicola De Stefano, Siena
#
# Copyright (C) 2005-2012 University of Oxford
#
# Part of FSL - FMRIB's Software Library
# http://www.fmrib.ox.ac.uk/fsl
# fsl@fmrib.ox.ac.uk
#
# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
# Imaging of the Brain), Department of Clinical Neurology, Oxford
# University, Oxford, UK
#
#
# LICENCE
#
# FMRIB Software Library, Release 5.0 (c) 2012, The University of
# Oxford (the "Software")
#
# The Software remains the property of the University of Oxford ("the
# University").
#
# The Software is distributed "AS IS" under this Licence solely for
# non-commercial use in the hope that it will be useful, but in order
# that the University as a charitable foundation protects its assets for
# the benefit of its educational and research purposes, the University
# makes clear that no condition is made or to be implied, nor is any
# warranty given or to be implied, as to the accuracy of the Software,
# or that it will be suitable for any particular purpose or for use
# under any specific conditions. Furthermore, the University disclaims
# all responsibility for the use which is made of the Software. It
# further disclaims any liability for the outcomes arising from using
# the Software.
#
# The Licensee agrees to indemnify the University and hold the
# University harmless from and against any and all claims, damages and
# liabilities asserted by third parties (including claims for
# negligence) which arise directly or indirectly from the use of the
# Software or the sale of any products based on the Software.
#
# No part of the Software may be reproduced, modified, transmitted or
# transferred in any form or by any means, electronic or mechanical,
# without the express permission of the University. The permission of
# the University is not required if the said reproduction, modification,
# transmission or transference is done without financial return, the
# conditions of this Licence are imposed upon the receiver of the
# product, and all original and amended source code is included in any
# transmitted product. You may be held legally responsible for any
# copyright infringement that is caused or encouraged by your failure to
# abide by these terms and conditions.
#
# You are not permitted under this Licence to use this Software
# commercially. Use for which any financial return is received shall be
# defined as commercial use, and includes (1) integration of all or part
# of the source code or the Software into a product for sale or license
# by or on behalf of Licensee to third parties or (2) use of the
# Software or any derivative of it for research with the final aim of
# developing software products for sale or license to a third party or
# (3) use of the Software or any derivative of it for research with the
# final aim of developing non-software products for sale or license to a
# third party, or (4) use of the Software to provide any service to an
# external organisation for which payment is received. If you are
# interested in using the Software commercially, please contact Isis
# Innovation Limited ("Isis"), the technology transfer company of the
# University, to negotiate a licence. Contact details are:
# innovation@isis.ox.ac.uk quoting reference DE/9564.
# {{{ Usage()
Usage() {
cat <<EOF
Usage: bet <input> <output> [options]
Main bet2 options:
-o generate brain surface outline overlaid onto original image
-m generate binary brain mask
-s generate approximate skull image
-n don't generate segmented brain image output
-f <f> fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates
-g <g> vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top
-r <r> head radius (mm not voxels); initial surface sphere is set to half of this
-c <x y z> centre-of-gravity (voxels not mm) of initial mesh surface.
-t apply thresholding to segmented brain image and mask
-e generates brain surface as mesh in .vtk format
Variations on default bet2 functionality (mutually exclusive options):
(default) just run bet2
-R robust brain centre estimation (iterates BET several times)
-S eye & optic nerve cleanup (can be useful in SIENA)
-B bias field & neck cleanup (can be useful in SIENA)
-Z improve BET if FOV is very small in Z (by temporarily padding end slices)
-F apply to 4D FMRI data (uses -f 0.3 and dilates brain mask slightly)
-A run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations)
-A2 <T2> as with -A, when also feeding in non-brain-extracted T2 (includes registrations)
Miscellaneous options:
-v verbose (switch on diagnostic messages)
-h display this help, then exits
-d debug (don't delete temporary intermediate images)
EOF
exit 1
}
# }}}
# {{{ get_dims()
get_dims() {
xdim=`${FSLDIR}/bin/fslval $1 dim1 | sed 's/-//g'`
ydim=`${FSLDIR}/bin/fslval $1 dim2 | sed 's/-//g'`
zdim=`${FSLDIR}/bin/fslval $1 dim3 | sed 's/-//g'`
xpixdim=`${FSLDIR}/bin/fslval $1 pixdim1 | sed 's/-//g'`
ypixdim=`${FSLDIR}/bin/fslval $1 pixdim2 | sed 's/-//g'`
zpixdim=`${FSLDIR}/bin/fslval $1 pixdim3 | sed 's/-//g'`
#echo $xdim $ydim $zdim $xpixdim $ypixdim $zpixdim
}
# }}}
# {{{ find_centre_in_mm()
# find_centre_in_mm() {
# centre=`${FSLDIR}/bin/fslstats $1 -l 0.001 -C`
# x=`echo $centre $xpixdim | awk '{print "10 k " $1 " " $4 " * p"}' | dc -`
# y=`echo $centre $ypixdim | awk '{print "10 k " $2 " " $4 " * p"}' | dc -`
# z=`echo $centre $zpixdim | awk '{print "10 k " $3 " " $4 " * p"}' | dc -`
# #echo $x $y $z
# }
# }}}
# {{{ find_centre_in_voxels()
find_centre_in_voxels() {
centre=`${FSLDIR}/bin/fslstats $1 -l 0.001 -C`
x=`echo $centre | awk '{print $1}'`
y=`echo $centre | awk '{print $2}'`
z=`echo $centre | awk '{print $3}'`
#echo $x $y $z
}
# }}}
# {{{ parse IN and OUT options
[ "$2" = "" ] && Usage
IN=`${FSLDIR}/bin/remove_ext $1`
OUT=`${FSLDIR}/bin/remove_ext $2`
shift 2
if [ `${FSLDIR}/bin/imtest $IN` = 0 ] ; then
echo ""
echo "Error: input image $IN not valid"
echo ""
exit 1
fi
# }}}
# {{{ setup variable defaults
debug=0
verbose=0
variation=0
skull=0
bet2opts=""
# }}}
# {{{ parse options
while [ _$1 != _ ] ; do
if [ $1 = -o ] || [ $1 = -m ] || [ $1 = -s ] || [ $1 = -n ] || [ $1 = -t ] || [ $1 = -e ] ; then
bet2opts="$bet2opts $1"
if [ $1 = -s ] ; then
skull=1
fi
shift
elif [ $1 = -f ] || [ $1 = -g ] || [ $1 = -r ] ; then
[ "$2" = "" ] && Usage
bet2opts="$bet2opts $1 $2"
shift 2
elif [ $1 = -c ] ; then
[ "$4" = "" ] && Usage
bet2opts="$bet2opts $1 $2 $3 $4"
shift 4
elif [ $1 = -R ] ; then
variation=1
shift
elif [ $1 = -S ] ; then
variation=2
shift
elif [ $1 = -Z ] ; then
variation=3
shift
elif [ $1 = -F ] ; then
variation=4
shift
elif [ $1 = -A ] ; then
variation=5
shift
elif [ $1 = -A2 ] ; then
[ "$2" = "" ] && Usage
variation=6
IN2=$2
shift 2
elif [ $1 = -B ] ; then
variation=7
shift
elif [ $1 = -v ] ; then
verbose=1
bet2opts="$bet2opts -v"
shift
elif [ $1 = -d ] ; then
debug=1
shift
else
Usage
fi
done
if [ $verbose = 1 ] ; then
echo IN=$IN
echo OUT=$OUT
echo bet2opts="${bet2opts}"
echo verbose=$verbose
echo debug=$debug
echo variation=$variation
fi
# }}}
# {{{ process variations
if [ $variation = 0 ] ; then
${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
elif [ $variation = 1 ] ; then
# {{{ BET robust
bet2opts=`echo $bet2opts | sed 's/-n//g'`
get_dims $IN
i=1
while [ $i -gt 0 ] ; do
#echo $i
if [ $i = 1 ] ; then
${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
find_centre_in_voxels $OUT
else
${FSLDIR}/bin/bet2 $IN $OUT $bet2opts -c $x $y $z
ox=$x; oy=$y; oz=$z;
find_centre_in_voxels $OUT
diffsq=`echo "0 k $ox $x - 2 ^ $oy $y - 2 ^ + $oz $z - 2 ^ + 1 / p" | dc -`
#echo $diffsq
if [ $diffsq -lt 1 ] || [ $i -gt 10 ] ; then
i=_10
fi
fi
i=`echo "$i 1 + p" | dc -`
done
# }}}
elif [ $variation = 2 ] ; then
# {{{ SIENA eye cleanup
#### get the raw brain and skull images
${FSLDIR}/bin/bet2 $IN ${OUT}_tmp_betraw -s $bet2opts
#### run betpremask (keep intermediate files around using -d) and feed it into bet
${FSLDIR}/bin/standard_space_roi $IN ${OUT}_tmp_premask -b -d
${FSLDIR}/bin/bet2 ${OUT}_tmp_premask ${OUT}_tmp_premask_bet -n -m -f 0.4 $bet2opts
#### bring eye mask from standard space into native and dilate, mostly in 2D and then invert
${FSLDIR}/bin/flirt -ref $IN -in ${FSLDIR}/data/standard/MNI152_T1_2mm_eye_mask -applyxfm -init ${OUT}_tmp_premask_tmp_to_std_inv.mat -datatype float -out ${OUT}_tmp_eye_mask
${FSLDIR}/bin/fslmaths ${OUT}_tmp_eye_mask -thr 0.5 -bin -dilF -kernel 2D -dilF -dilF -dilF -dilF -dilF -dilF -dilF ${OUT}_tmp_eyes7dil -odt short
${FSLDIR}/bin/fslmaths ${OUT}_tmp_eyes7dil -mul -1 -add 1 ${OUT}_tmp_eyes7dil_inv
#### mask original brain mask with inverted-eye-mask, ADD betpremask_bet_mask and X by original brain
${FSLDIR}/bin/fslmaths ${OUT}_tmp_betraw -bin -mas ${OUT}_tmp_eyes7dil_inv -add ${OUT}_tmp_premask_bet_mask -bin -mul ${OUT}_tmp_betraw ${OUT}_tmp_prebrain
#### find upper threshold used to delete eyes
Mean=`${FSLDIR}/bin/fslstats ${OUT}_tmp_prebrain -M`
SD=`${FSLDIR}/bin/fslstats ${OUT}_tmp_prebrain -S`
thr=`echo "10 k 3.5 $SD * $Mean + p" | dc -`
#### apply threshold and a little morphology (twice) to cleanup further and produce final brain image
${FSLDIR}/bin/fslmaths ${OUT}_tmp_prebrain -uthr $thr -bin -ero -dilF -dilF -ero -mul ${OUT}_tmp_prebrain -uthr $thr -bin -kernel 2D -ero -dilF -mul ${OUT}_tmp_betraw $OUT
${FSLDIR}/bin/fslmaths $OUT -bin ${OUT}_mask
#### remove eyes from original skull to produce final skull image
${FSLDIR}/bin/fslmaths ${OUT}_tmp_eyes7dil -ero -kernel 2D -ero -mul -1 -add 1 ${OUT}_tmp_eyes5dil_inv
${FSLDIR}/bin/fslmaths ${OUT}_tmp_betraw_skull -mas ${OUT}_tmp_eyes5dil_inv ${OUT}_skull
# }}}
elif [ $variation = 3 ] ; then
# {{{ small FOV in Z
MINZFOV=100.0
get_dims $IN
npad=`echo "$MINZFOV $zpixdim / $zdim - 2 / 1 + p" | dc -`
if [ $npad -le 0 ] ; then
echo "Image already has a greater Z FOV than $MINZFOV so not using padding"
${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
exit
fi
${FSLDIR}/bin/fslroi $IN ${OUT}_tmp_bottom 0 $xdim 0 $ydim 0 1
${FSLDIR}/bin/fslroi $IN ${OUT}_tmp_top 0 $xdim 0 $ydim `echo "$zdim 1 - p" | dc -` 1
n=1
while [ $n -le $npad ] ; do
bottomlist="$bottomlist ${OUT}_tmp_bottom"
toplist="$toplist ${OUT}_tmp_top"
n=`echo "$n 1 + p" | dc -`
done
${FSLDIR}/bin/fslmerge -z ${OUT}_tmp $bottomlist $IN $toplist
${FSLDIR}/bin/bet2 ${OUT}_tmp $OUT $bet2opts
for f in `imglob ${OUT}*` ; do
${FSLDIR}/bin/fslroi $f $f 0 $xdim 0 $ydim $npad $zdim
done
# }}}
elif [ $variation = 4 ] ; then
# {{{ FMRI
${FSLDIR}/bin/fslroi $IN ${OUT}_tmp 0 1
${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
# }}}
elif [ $variation = 5 ] ; then
# {{{ bet2 + betsurf (T1 only)
# register T1 to standard space
${FSLDIR}/bin/flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm -in $IN -omat ${OUT}_tmp_T1_to_std.mat
# run brain extraction and save brain mesh
${FSLDIR}/bin/bet2 $IN $OUT -e $bet2opts
# find other surfaces
${FSLDIR}/bin/betsurf --t1only -o -m -s $IN ${OUT}_mesh.vtk ${OUT}_tmp_T1_to_std.mat $OUT
# }}}
elif [ $variation = 6 ] ; then
# {{{ bet2 + betsurf (T1 & T2)
# register T2 to T1
${FSLDIR}/bin/flirt -in $IN2 -ref $IN -out ${OUT}_tmp_T2_to_T1 -omat ${OUT}_tmp_T2_to_T1.mat -interp sinc
# register T1 to standard space
${FSLDIR}/bin/flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm -in $IN -omat ${OUT}_tmp_T1_to_std.mat
# run brain extraction and save brain mesh
${FSLDIR}/bin/bet2 $IN $OUT -e $bet2opts
# find other surfaces
${FSLDIR}/bin/betsurf -o -m -s $IN ${OUT}_tmp_T2_to_T1 ${OUT}_mesh.vtk ${OUT}_tmp_T1_to_std.mat $OUT
# }}}
elif [ $variation = 7 ] ; then
# {{{ SIENA bias field & neck cleanup
#### run betpremask
${FSLDIR}/bin/standard_space_roi $IN ${OUT}_tmp_premask -b -d
#### run FAST to get bias field
${FSLDIR}/bin/fast -b ${OUT}_tmp_premask >/dev/null 2>&1
#### apply bias correction to original
${FSLDIR}/bin/fslmaths $IN -div ${OUT}_tmp_premask_bias ${OUT}_tmp_unbiased
#### get skull if asked for
if [ $skull ] ; then
${FSLDIR}/bin/standard_space_roi ${OUT}_tmp_unbiased ${OUT}_tmp_unbiased_forskull_reduced -maskFOV -roiNONE -d
${FSLDIR}/bin/bet2 ${OUT}_tmp_unbiased_forskull_reduced ${OUT}_tmp_unbiased_forskull $bet2opts
bet2opts=`echo $bet2opts | sed 's/-s//g'`
${FSLDIR}/bin/immv ${OUT}_tmp_unbiased_forskull_skull ${OUT}_skull
fi
#### re-run betpremask
${FSLDIR}/bin/standard_space_roi ${OUT}_tmp_unbiased ${OUT}_tmp_unbiased_premask -b -d
#### re-run in robust mode
${FSLDIR}/bin/bet ${OUT}_tmp_unbiased_premask $OUT -m $bet2opts -R -d
# }}}
fi
# }}}
# {{{ cleanup temporary files
if [ $debug = 0 ] ; then
/bin/rm -f ${OUT}_tmp*
fi
# }}}