forked from ANTsX/ANTs
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbuildtemplateparallel.sh
executable file
·1393 lines (1114 loc) · 49.5 KB
/
buildtemplateparallel.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
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
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#!/bin/bash
VERSION="0.0.14 test"
afftype=".txt"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
function setPath {
cat <<SETPATH
--------------------------------------------------------------------------------------
Error locating ANTS
--------------------------------------------------------------------------------------
It seems that the ANTSPATH environment variable is not set. Please add the ANTSPATH
variable. This can be achieved by editing the .bash_profile in the home directory.
Add:
ANTSPATH=/home/yourname/bin/ants/
Or the correct location of the ANTS binaries.
Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
SETPATH
exit 1
}
# Uncomment the line below in case you have not set the ANTSPATH variable in your environment.
# export ANTSPATH=${ANTSPATH:="$HOME/bin/ants/"} # EDIT THIS
#ANTSPATH=YOURANTSPATH
if [ ${#ANTSPATH} -le 3 ]
then
setPath >&2
fi
if [ ! -s ${ANTSPATH}/ANTS ] ; then
echo "ANTS program can't be found. Please (re)define \$ANTSPATH in your environment."
exit
fi
# Test availability of helper scripts.
# No need to test this more than once. Can reside outside of the main loop.
ANTSSCRIPTNAME=${ANTSPATH}/antsIntroduction.sh
PEXEC=${ANTSPATH}/ANTSpexec.sh
SGE=${ANTSPATH}/waitForSGEQJobs.pl
PBS=${ANTSPATH}/waitForPBSQJobs.pl
XGRID=${ANTSPATH}/waitForXGridJobs.pl
SLURM=${ANTSPATH}/waitForSlurmJobs.pl
fle_error=0
for FLE in $ANTSSCRIPTNAME $PEXEC $SGE $XGRID $SLURM
do
if [ ! -x $FLE ] ;
then
echo
echo "--------------------------------------------------------------------------------------"
echo " FILE $FLE DOES NOT EXIST -- OR -- IS NOT EXECUTABLE !!! $0 will terminate."
echo "--------------------------------------------------------------------------------------"
echo " if the file is not executable, please change its permissions. "
fle_error=1
fi
done
if [ $fle_error = 1 ] ; then
exit 1
fi
#assuming .nii.gz as default file type. This is the case for ANTS 1.7 and up
function Usage {
cat <<USAGE
Usage:
`basename $0` -d ImageDimension -o OUTPREFIX <other options> <images>
Compulsory arguments (minimal command line requires SGE cluster, otherwise use -c & -j options):
-d: ImageDimension: 2 or 3 (for 2 or 3 dimensional registration of single volume)
ImageDimension: 4 (for template generation of time-series data)
-o: OUTPREFIX; A prefix that is prepended to all output files.
<images> List of images in the current directory, eg *_t1.nii.gz. Should be at the end
of the command.
NB: All images to be added to the template should be in the same directory, and this script
should be invoked from that directory.
Optional arguments:
-c: Control for parallel computation (default 1) -- 0 == run serially, 1 == SGE qsub,
2 == use PEXEC (localhost), 3 == Apple XGrid, 4 == PBS qsub, 5 == SLURM
-q: Set default queue for PBS jobs (default: nopreempt)
-g: Gradient step size (default 0.25) for template update. Does not affect the step size of individual registrations. The
default of 0.25 should not be increased, smaller numbers result in more cautious template update steps.
-i: Iteration limit (default 4) -- iterations of the template construction (Iteration limit)*NumImages registrations.
-j: Number of cpu cores to use (default: 2; -- requires "-c 2")
-m: Max-iterations in each registration, eg 30x90x30
-n: N4BiasFieldCorrection of moving image (default 1) -- 0 == off, 1 == on. If 1, will run N4 before each registration. It is
more efficient to run N4BiasFieldCorrection on the input images once, then build a template from the corrected images.
-p: Commands to prepend to job scripts (e.g., change into appropriate directory, set paths, etc)
-r: Do rigid-body registration of inputs before creating template (default 0) -- 0 == off 1 == on. Only useful when
you do not have an initial template
-s: Type of similarity metric used for registration.
-t: Type of transformation model used for registration.
-x: XGrid arguments (e.g., -x "-p password -h controlhost")
-z: Use this this volume as the target of all inputs. When not used, the script
will create an unbiased starting point by averaging all inputs. Use the full path!
If you do not have an initial template, it is advisible to run a few iterations with affine
normalization only (-m 1x0x0) to get a sensible initial template, then pass this with -z
to run full deformable registration.
Example:
`basename $0` -d 3 -m 30x50x20 -t GR -s CC -c 1 -o MY -z InitialTemplate.nii.gz *RF*T1x.nii.gz
- In this example 30x50x20 iterations per registration are used for template creation (that is the default)
- Greedy-SyN and CC are the metrics to guide the mapping.
- Output is prepended with MY and the initial template is InitialTemplate.nii.gz (optional).
- The -c option is set to 1, which will result in using the Sun Grid Engine (SGE) to distribute the computation.
- if you do not have SGE, read the help for multi-core computation on the local machine, or Apple X-grid options.
--------------------------------------------------------------------------------------
ANTS was created by:
--------------------------------------------------------------------------------------
Brian B. Avants, Nick Tustison and Gang Song
Penn Image Computing And Science Laboratory
University of Pennsylvania
Please reference http://www.ncbi.nlm.nih.gov/pubmed/20851191 when employing this script
in your studies. A reproducible evaluation of ANTs similarity metric performance in
brain image registration:
* Avants BB, Tustison NJ, Song G, Cook PA, Klein A, Gee JC. Neuroimage, 2011.
Also see http://www.ncbi.nlm.nih.gov/pubmed/19818860 for more details.
The script has been updated and improved since this publication.
--------------------------------------------------------------------------------------
script adapted by N.M. van Strien, http://www.mri-tutorial.com | NTNU MR-Center
--------------------------------------------------------------------------------------
Apple XGrid support by Craig Stark
--------------------------------------------------------------------------------------
USAGE
exit 1
}
function Help {
cat <<HELP
`basename $0` will make a template out of the input files using an elastic
or diffeomorphic transformation. This script builds a template iteratively from the input
images and uses Sun Grid Engine (SGE) or multiple cpu cores on the localhost (min 2) to
parallelize the registration of each subject to the template.
Usage:
`basename $0` -d ImageDimension -o OUTPREFIX <other options> <images>
Example Case:
bash `basename $0` -d 3 -m 30x50x20 -t GR -s CC -c 1 -o MY -z InitialTemplate.nii.gz *RF*T1x.nii.gz
- In this case you use 30x50x20 iterations per registration
- 4 iterations over template creation (that is the default)
- With Greedy-SyN and CC metrics to guide the mapping.
- Output is prepended with MY and the initial template is InitialTemplate.nii.gz (optional).
- The -c option is set to 1 which will try to use SGE to distribute the computation.
- If you do not have SGE, use -c 0 or -c 2 combined with -j.
- Continue reading this help file if things are not yet clear.
Compulsory arguments (minimal command line requires SGE cluster, otherwise use -c & -j options)::
-d: ImageDimension: 2 or 3 (for 2 or 3 dimensional registration of single volume)
ImageDimension: 4 (for template generation of time-series data)
-o: OUTPREFIX; A prefix that is prepended to all output files.
<images> List of images in the current directory, eg *_t1.nii.gz. Should be at the end
of the command.
NB: All files to be added to the template should be in the same directory.
Optional arguments:
-c: Control for parallel computation (default 1) -- 0 == run serially, 1 == SGE qsub,
2 == use PEXEC (localhost), 3 == Apple XGrid, 4 == PBS Grid, 5 == SLURM
-g: Gradient step size; smaller in magnitude results in more cautious steps (default 0.25). This does not affect the step size
of individual registrations; it lets you update the template more cautiously after each iteration by reducing the template
update step size from 0.25 to a smaller positive number.
-i: Iteration limit (default = 4) for template construction. requires 4*NumImages registrations.
-j: Number of cpu cores to use (default: 2; --- set -c option to 2 to use this .
The optimal number of cpu cores to use for template generation depends on the availability of cores, the amount of
free working memory (RAM) and the resolution of the data. High resolution datasets typically require more RAM during
processing. Running out of RAM during a calculation will slow down all processing on your computer.
-m: Max-iterations
Max-Iterations in form: JxKxL where
J = max iterations at coarsest resolution (here, reduce by power of 2^2)
K = middle resolution iterations (here,reduce by power of 2)
L = fine resolution iterations (here, full resolution) !!this level takes much
more time per iteration!!
Adding an extra value before JxKxL (i.e. resulting in IxJxKxL) would add another
iteration level.
-n: N4BiasFieldCorrection of moving image ( 0 = off; 1 = on (default) )
-p: Commands to prepend to job scripts (e.g., change into appropriate directory, set paths, etc)
-r: Do rigid-body registration of inputs before creating template (default 0) -- 0 == off 1 == on. Only useful when
you do not have an initial template
In case a template is specified (-z option), all inputs are registered to that template. If
no template is specified, the inputs will be registered to the averaged input.
-s: Type of similarity metric used for registration.
For intramodal image registration, use:
CC = cross-correlation
MI = mutual information
PR = probability mapping (default)
MSQ = mean square difference (Demons-like)
SSD = sum of squared differences
For intermodal image registration, use:
MI = mutual information
PR = probability mapping (default)
-t: Type of transformation model used for registration.
For rigid image registration, use:
RI = Purely rigid
RA = Affine rigid
For elastic image registration, use:
EL = elastic transformation model (less deformation possible)
For diffeomorphic image registration, use:
SY = SyN with time (default) with arbitrary number of time points in time discretization
S2 = SyN with time optimized specifically for 2 time points in the time discretization
GR = Greedy SyN
EX = Exponential
DD = Diffeomorphic Demons style exponential mapping
-x: XGrid arguments (e.g., -x "-p password -h controlhost")
-z: Use this this volume as the target of all inputs. When not used, the script
will create an unbiased starting point by averaging all inputs. Use the full path!
If you do not have an initial template, it is advisible to run a few iterations with affine
normalization only (-m 1x0x0) to get a sensible initial template, then pass this with -z
to run full deformable registration.
Requirements:
This scripts relies on the following scripts in your $ANTSPATH directory. The script
will terminate prematurely if these files are not present or are not executable.
- antsIntroduction.sh
- pexec.sh
- waitForSGEQJobs.pl (only for use with Sun Grid Engine)
- ANTSpexec.sh (only for use with localhost parallel execution)
- waitForXGridJobs.pl (only for use with Apple XGrid)
- waitForSlurmJobs.pl (only for use with SLURM)
--------------------------------------------------------------------------------------
Get the latest ANTS version at:
--------------------------------------------------------------------------------------
http://sourceforge.net/projects/advants/
--------------------------------------------------------------------------------------
Read the ANTS documentation at:
--------------------------------------------------------------------------------------
http://picsl.upenn.edu/ANTS/
--------------------------------------------------------------------------------------
ANTS was created by:
--------------------------------------------------------------------------------------
Brian B. Avants, Nick Tustison and Gang Song
Penn Image Computing And Science Laboratory
University of Pennsylvania
Please reference http://www.ncbi.nlm.nih.gov/pubmed/20851191 when employing this script
in your studies. A reproducible evaluation of ANTs similarity metric performance in
brain image registration:
* Avants BB, Tustison NJ, Song G, Cook PA, Klein A, Gee JC. Neuroimage, 2011.
Also see http://www.ncbi.nlm.nih.gov/pubmed/19818860 for more details.
The script has been updated and improved since this publication.
--------------------------------------------------------------------------------------
script adapted by N.M. van Strien, http://www.mri-tutorial.com | NTNU MR-Center
--------------------------------------------------------------------------------------
Apple XGrid support by Craig Stark
--------------------------------------------------------------------------------------
HELP
exit 1
}
function reportMappingParameters {
cat <<REPORTMAPPINGPARAMETERS
--------------------------------------------------------------------------------------
Mapping parameters
--------------------------------------------------------------------------------------
ANTSPATH is $ANTSPATH
Dimensionality: $DIM
N4BiasFieldCorrection: $N4CORRECT
Similarity Metric: $METRICTYPE
Transformation: $TRANSFORMATIONTYPE
Regularization: $REGULARIZATION
MaxIterations: $MAXITERATIONS
Number Of MultiResolution Levels: $NUMLEVELS
OutputName prefix: $OUTPUTNAME
Template: $TEMPLATE
Template Update Steps: $ITERATIONLIMIT
Template population: $IMAGESETVARIABLE
--------------------------------------------------------------------------------------
REPORTMAPPINGPARAMETERS
}
function shapeupdatetotemplate {
# local declaration of values
dim=${DIM}
template=${TEMPLATE}
templatename=${TEMPLATENAME}
outputname=${OUTPUTNAME}
gradientstep=-${GRADIENTSTEP}
# debug only
# echo $dim
# echo ${template}
# echo ${templatename}
# echo ${outputname}
# echo ${outputname}*formed.nii*
# echo ${gradientstep}
# We find the average warp to the template and apply its inverse to the template image
# This keeps the template shape stable over multiple iterations of template building
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate 1"
echo "--------------------------------------------------------------------------------------"
${ANTSPATH}/AverageImages $dim ${template} 1 ${outputname}*formed.nii.gz
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate 2"
echo "--------------------------------------------------------------------------------------"
${ANTSPATH}/AverageImages $dim ${templatename}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate 3"
echo "--------------------------------------------------------------------------------------"
${ANTSPATH}/MultiplyImages $dim ${templatename}warp.nii.gz ${gradientstep} ${templatename}warp.nii.gz
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate 4"
echo "--------------------------------------------------------------------------------------"
rm -f ${templatename}Affine${afftype}
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate 5"
echo "--------------------------------------------------------------------------------------"
# Averaging and inversion code --- both are 1st order estimates.
# if [ ${dim} -eq 2 ] ; then
# ANTSAverage2DAffine ${templatename}Affine${afftype} ${outputname}*Affine${afftype}
# elif [ ${dim} -eq 3 ] ; then
# ANTSAverage3DAffine ${templatename}Affine${afftype} ${outputname}*Affine${afftype}
# fi
${ANTSPATH}/AverageAffineTransform ${dim} ${templatename}Affine${afftype} ${outputname}*Affine${afftype}
${ANTSPATH}/WarpImageMultiTransform ${dim} ${templatename}warp.nii.gz ${templatename}warp.nii.gz -i ${templatename}Affine${afftype} -R ${template}
${ANTSPATH}/WarpImageMultiTransform ${dim} ${template} ${template} -i ${templatename}Affine${afftype} ${templatename}warp.nii.gz ${templatename}warp.nii.gz ${templatename}warp.nii.gz ${templatename}warp.nii.gz -R ${template}
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate 6"
echo "--------------------------------------------------------------------------------------"
echo
${ANTSPATH}/MeasureMinMaxMean ${dim} ${templatename}warp.nii.gz ${templatename}warplog.txt 1
}
function ANTSAverage2DAffine {
OUTNM=${templatename}Affine${afftype}
FLIST=${outputname}*Affine${afftype}
NFILES=0
PARAM1=0
PARAM2=0
PARAM3=0
PARAM4=0
PARAM5=0
PARAM6=0
PARAM7=0
PARAM8=0
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2 `
for x in $LL ; do PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ; let NFILES=$NFILES+1 ; done
PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3 `
for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4 `
for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5 `
for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6 `
for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM5=0 # ` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7 `
for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM6=0 # ` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2 `
for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3 `
for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
echo "# Insight Transform File V1.0 " > $OUTNM
echo "# Transform 0 " >> $OUTNM
echo "Transform: MatrixOffsetTransformBase_double_2_2 " >> $OUTNM
echo "Parameters: $PARAM1 $PARAM2 $PARAM3 $PARAM4 $PARAM5 $PARAM6 " >> $OUTNM
echo "FixedParameters: $PARAM7 $PARAM8 " >> $OUTNM
}
function ANTSAverage3DAffine {
OUTNM=${templatename}Affine${afftype}
FLIST=${outputname}*Affine${afftype}
NFILES=0
PARAM1=0
PARAM2=0
PARAM3=0
PARAM4=0
PARAM5=0
PARAM6=0
PARAM7=0
PARAM8=0
PARAM9=0
PARAM10=0
PARAM11=0
PARAM12=0
PARAM13=0
PARAM14=0
PARAM15=0
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 2 `
for x in $LL ; do PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ; let NFILES=$NFILES+1 ; done
PARAM1=` awk -v a=$PARAM1 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 3 `
for x in $LL ; do PARAM2=` awk -v a=$PARAM2 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM2=` awk -v a=$PARAM2 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 4 `
for x in $LL ; do PARAM3=` awk -v a=$PARAM3 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM3=` awk -v a=$PARAM3 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 5 `
for x in $LL ; do PARAM4=` awk -v a=$PARAM4 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM4=` awk -v a=$PARAM4 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 6 `
for x in $LL ; do PARAM5=` awk -v a=$PARAM5 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM5=` awk -v a=$PARAM5 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 7 `
for x in $LL ; do PARAM6=` awk -v a=$PARAM6 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM6=` awk -v a=$PARAM6 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 8 `
for x in $LL ; do PARAM7=` awk -v a=$PARAM7 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM7=` awk -v a=$PARAM7 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 9 `
for x in $LL ; do PARAM8=` awk -v a=$PARAM8 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM8=` awk -v a=$PARAM8 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 10 `
for x in $LL ; do PARAM9=` awk -v a=$PARAM9 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM9=` awk -v a=$PARAM9 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 11 `
for x in $LL ; do PARAM10=` awk -v a=$PARAM10 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM10=0 # ` awk -v a=$PARAM10 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 12 `
for x in $LL ; do PARAM11=` awk -v a=$PARAM11 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM11=0 # ` awk -v a=$PARAM11 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` head -n 4 $FLIST | grep Paramet | cut -d ' ' -f 13 `
for x in $LL ; do PARAM12=` awk -v a=$PARAM12 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM12=0 # ` awk -v a=$PARAM12 -v b=$NFILES 'BEGIN{print (a / b)}' `
# origin params below
LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 2 `
for x in $LL ; do PARAM13=` awk -v a=$PARAM13 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM13=` awk -v a=$PARAM13 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 3 `
for x in $LL ; do PARAM14=` awk -v a=$PARAM14 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM14=` awk -v a=$PARAM14 -v b=$NFILES 'BEGIN{print (a / b)}' `
LL=` cat $FLIST | grep FixedParamet | cut -d ' ' -f 4 `
for x in $LL ; do PARAM15=` awk -v a=$PARAM15 -v b=$x 'BEGIN{print (a + b)}' ` ; done
PARAM15=` awk -v a=$PARAM15 -v b=$NFILES 'BEGIN{print (a / b)}' `
echo "# Insight Transform File V1.0 " > $OUTNM
echo "# Transform 0 " >> $OUTNM
echo "Transform: MatrixOffsetTransformBase_double_3_3 " >> $OUTNM
echo "Parameters: $PARAM1 $PARAM2 $PARAM3 $PARAM4 $PARAM5 $PARAM6 $PARAM7 $PARAM8 $PARAM9 $PARAM10 $PARAM11 $PARAM12 " >> $OUTNM
echo "FixedParameters: $PARAM13 $PARAM14 $PARAM15 " >> $OUTNM
}
function jobfnamepadding {
files=`ls job*.sh`
BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
for file in ${files}
do
if [ "${#file}" -eq "9" ]
then
BASENAME2=`echo $file | cut -d 'b' -f 2 `
mv "$file" "${BASENAME1}b_000${BASENAME2}"
elif [ "${#file}" -eq "10" ]
then
BASENAME2=`echo $file | cut -d 'b' -f 2 `
mv "$file" "${BASENAME1}b_00${BASENAME2}"
elif [ "${#file}" -eq "11" ]
then
BASENAME2=`echo $file | cut -d 'b' -f 2 `
mv "$file" "${BASENAME1}b_0${BASENAME2}"
fi
done
}
cleanup()
# example cleanup function
{
cd ${currentdir}/
echo -en "\n*** Performing cleanup, please wait ***\n"
# 1st attempt to kill all remaining processes
# put all related processes in array
runningANTSpids=( `ps -C ANTS -C N4BiasFieldCorrection -C ImageMath| awk '{ printf "%s\n", $1 ; }'` )
# debug only
#echo list 1: ${runningANTSpids[@]}
# kill these processes, skip the first since it is text and not a PID
for ((i = 1; i < ${#runningANTSpids[@]} ; i++))
do
echo "killing: ${runningANTSpids[${i}]}"
kill ${runningANTSpids[${i}]}
done
return $?
}
control_c()
# run if user hits control-c
{
echo -en "\n*** User pressed CTRL + C ***\n"
cleanup
if [ $DOQSUB -eq 1 ] ; then
qdel $jobIDs
elif [ $DOQSUB -eq 5 ]; then
scancel $jobIDs
fi
exit $?
echo -en "\n*** Script cancelled by user ***\n"
}
#initializing variables with global scope
time_start=`date +%s`
currentdir=`pwd`
nargs=$#
MAXITERATIONS=30x90x20
LABELIMAGE=0 # initialize optional parameter
METRICTYPE=CC # initialize optional parameter
TRANSFORMATIONTYPE="GR" # initialize optional parameter
if [[ $dim == 4 ]] ; then
# we use a more constrained regularization for 4D mapping b/c we expect deformations to be relatively small and local
TRANSFORMATIONTYPE="GR_Constrained"
fi
N4CORRECT=1 # initialize optional parameter
DEFQUEUE=nopreempt
DOQSUB=1 # By default, buildtemplateparallel tries to do things in parallel
GRADIENTSTEP=0.25 # Gradient step size, smaller in magnitude means more smaller (more cautious) steps
ITERATIONLIMIT=4
CORES=2
TDIM=0
RIGID=0
RIGIDTYPE=" --do-rigid" # set to an empty string to use affine initialization
range=0
REGTEMPLATE=target
XGRIDOPTS=""
SCRIPTPREPEND=""
# System specific queue options, eg "-q name" to submit to a specific queue
# It can be set to an empty string if you do not need any special cluster options
QSUBOPTS="" # EDIT THIS
OUTPUTNAME=antsBTP
##Getting system info from linux can be done with these variables.
# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
# cpu_free_ram=$((${RAMfree}/${cpu_count}))
if [ ${OSTYPE:0:6} == 'darwin' ]
then
cpu_count=`sysctl -n hw.physicalcpu`
else
cpu_count=`cat /proc/cpuinfo | grep processor | wc -l`
fi
# Provide output for Help
if [ "$1" == "-h" ]
then
Help >&2
fi
# reading command line arguments
while getopts "c:q:d:g:i:j:h:m:n:o:p:s:r:t:x:z:" OPT
do
case $OPT in
h) #help
echo "$USAGE"
exit 0
;;
c) #use SGE cluster
DOQSUB=$OPTARG
if [[ ${#DOQSUB} -gt 2 ]] ; then
echo " DOQSUB must be an integer value (0=serial, 1=SGE qsub, 2=try pexec, 3=XGrid, 4=PBS qsub, 5=SLURM) you passed -c $DOQSUB "
exit 1
fi
;;
q) #override default qsub queue
DEFQUEUE=$OPTARG
;;
d) #dimensions
DIM=$OPTARG
if [[ ${DIM} -eq 4 ]] ; then
DIM=3
TDIM=4
fi
;;
g) #gradient stepsize (default = 0.25)
GRADIENTSTEP=$OPTARG
;;
i) #iteration limit (default = 3)
ITERATIONLIMIT=$OPTARG
;;
j) #number of cpu cores to use (default = 2)
CORES=$OPTARG
;;
m) #max iterations other than default
MAXITERATIONS=$OPTARG
;;
n) #apply bias field correction
N4CORRECT=$OPTARG
;;
o) #output name prefix
OUTPUTNAME=$OPTARG
TEMPLATENAME=${OUTPUTNAME}template
TEMPLATE=${TEMPLATENAME}.nii.gz
;;
p) #Script prepend
SCRIPTPREPEND=$OPTARG
;;
s) #similarity model
METRICTYPE=$OPTARG
;;
r) #start with rigid-body registration
RIGID=$OPTARG
;;
t) #transformation model
TRANSFORMATIONTYPE=$OPTARG
;;
x) #initialization template
XGRIDOPTS=$XGRIDOPTS
;;
z) #initialization template
REGTEMPLATE=$OPTARG
;;
\?) # getopts issues an error message
echo "$USAGE" >&2
exit 1
;;
esac
done
# Provide different output for Usage and Help
if [ ${TDIM} -eq 4 ] && [ $nargs -lt 5 ]
then
Usage >&2
elif [ ${TDIM} -eq 4 ] && [ $nargs -eq 5 ]
then
echo ""
# This option is required to run 4D template creation on SGE with a minimal command line
elif [ $nargs -lt 6 ]
then
Usage >&2
fi
if [[ $DOQSUB -eq 1 || $DOQSUB -eq 4 ]] ; then
qq=`which qsub`
if [ ${#qq} -lt 1 ] ; then
echo do you have qsub? if not, then choose another c option ... if so, then check where the qsub alias points ...
exit
fi
fi
if [[ $DOQSUB -eq 5 ]]; then
qq=`which sbatch`
if [[ ${#qq} -lt 1 ]]; then
echo "do you have sbatch? if not, then choose another c option ... if so, then check where the sbatch alias points ..."
exit
fi
fi
# Creating the file list of images to make a template from.
# Shiftsize is calculated because a variable amount of arguments can be used on the command line.
# The shiftsize variable will give the correct number of arguments to skip. Issuing shift $shiftsize will
# result in skipping that number of arguments on the command line, so that only the input images remain.
shiftsize=$(($OPTIND - 1))
shift $shiftsize
# The invocation of $* will now read all remaining arguments into the variable IMAGESETVARIABLE
IMAGESETVARIABLE=$*
NINFILES=$(($nargs - $shiftsize))
# FSL not needed anymore, all dependent on ImageMath
# #test if FSL is available in case of 4D, exit if not
# if [ ${TDIM} -eq 4 ] && [ ${#FSLDIR} -le 0 ]
# then
# setFSLPath >&2
# fi
if [ ${NINFILES} -eq 0 ]
then
echo "Please provide at least 2 filenames for the template."
echo "Use `basename $0` -h for help"
exit 1
elif [[ ${NINFILES} -eq 1 ]]
then
range=`${ANTSPATH}/ImageMath $TDIM abs nvols ${IMAGESETVARIABLE} | tail -1 | cut -d "," -f 4 | cut -d " " -f 2 | cut -d "]" -f 1 `
if [ ${range} -eq 1 ] && [ ${TDIM} -ne 4 ]
then
echo "Please provide at least 2 filenames for the template."
echo "Use `basename $0` -h for help"
exit 1
elif [ ${range} -gt 1 ] && [ ${TDIM} -ne 4 ]
then
echo "This is a multivolume file. Use -d 4"
echo "Use `basename $0` -h for help"
exit 1
elif [ ${range} -gt 1 ] && [ ${TDIM} -eq 4 ]
then
echo
echo "--------------------------------------------------------------------------------------"
echo " Creating template of 4D input. "
echo "--------------------------------------------------------------------------------------"
#splitting volume
#setting up working dirs
tmpdir=${currentdir}/tmp_${RANDOM}_${RANDOM}_${RANDOM}_$$
(umask 077 && mkdir ${tmpdir}) || {
echo "Could not create temporary directory! Exiting." 1>&2
exit 1
}
mkdir ${tmpdir}/selection
#split the 4D file into 3D elements
cp ${IMAGESETVARIABLE} ${tmpdir}/
cd ${tmpdir}/
# ${ANTSPATH}/ImageMath $TDIM vol0.nii.gz TimeSeriesSubset ${IMAGESETVARIABLE} ${range}
# rm -f ${IMAGESETVARIABLE}
# selecting 16 volumes randomly from the timeseries for averaging, placing them in tmp/selection folder.
# the script will automatically divide timeseries into $total_volumes/16 bins from wich to take the random volumes;
# if there are more than 32 volumes in the time-series (in case they are smaller
nfmribins=2
let
if [ ${range} -gt 31 ] ; then
BINSIZE=$((${range} / ${nfmribins}))
j=1 # initialize counter j
for ((i = 0; i < ${nfmribins} ; i++))
do
FLOOR=$((${i} * ${BINSIZE}))
BINrange=$((${j} * ${BINSIZE}))
# Retrieve random number between two limits.
number=0 #initialize
while [ "$number" -le $FLOOR ]
do
number=$RANDOM
if [ $i -lt 15 ]
then
let "number %= $BINrange" # Scales $number down within $range.
elif [ $i -eq 15 ]
then
let "number %= $range" # Scales $number down within $range.
fi
done
#debug only
echo
echo "Random number between $FLOOR and $BINrange --- $number"
# echo "Random number between $FLOOR and $range --- $number"
if [ ${number} -lt 10 ]
then
${ANTSPATH}/ImageMath $TDIM selection/vol000${number}.nii.gz ExtractSlice ${IMAGESETVARIABLE} ${number}
# cp vol000${number}.nii.gz selection/
elif [ ${number} -ge 10 ] && [ ${number} -lt 100 ]
then
${ANTSPATH}/ImageMath $TDIM selection/vol00${number}.nii.gz ExtractSlice ${IMAGESETVARIABLE} ${number}
# cp vol00${number}.nii.gz selection/
elif [ ${number} -ge 100 ] && [ ${number} -lt 1000 ]
then
${ANTSPATH}/ImageMath $TDIM selection/vol0${number}.nii.gz ExtractSlice ${IMAGESETVARIABLE} ${number}
# cp vol0${number}.nii.gz selection/
fi
let j++
done
elif [ ${range} -gt ${nfmribins} ] && [ ${range} -lt 32 ]
then
for ((i = 0; i < ${nfmribins} ; i++))
do
number=$RANDOM
let "number %= $range"
if [ ${number} -lt 10 ]
then
${ANTSPATH}/ImageMath $TDIM selection/vol0.nii.gz ExtractSlice ${IMAGESETVARIABLE} ${number}
# cp vol000${number}.nii.gz selection/
elif [ ${number} -ge 10 ] && [ ${number} -lt 100 ]
then
${ANTSPATH}/ImageMath $TDIM selection/vol0.nii.gz ExtractSlice ${IMAGESETVARIABLE} ${number}
# cp vol00${number}.nii.gz selection/
fi
done
elif [ ${range} -le ${nfmribins} ]
then
${ANTSPATH}/ImageMath selection/$TDIM vol0.nii.gz TimeSeriesSubset ${IMAGESETVARIABLE} ${range}
# cp *.nii.gz selection/
fi
# set filelist variable
rm -f ${IMAGESETVARIABLE}
cd selection/
IMAGESETVARIABLE=`ls *.nii.gz`
fi
fi
# exit
# check for an initial template image and perform rigid body registration if requested
if [ ! -s $REGTEMPLATE ]
then
echo
echo "--------------------------------------------------------------------------------------"
echo " No initial template exists. Creating a population average image from the inputs."
echo "--------------------------------------------------------------------------------------"
${ANTSPATH}/AverageImages $DIM $TEMPLATE 1 $IMAGESETVARIABLE
else
echo
echo "--------------------------------------------------------------------------------------"
echo " Initial template found. This will be used for guiding the registration. use : $REGTEMPLATE and $TEMPLATE "
echo "--------------------------------------------------------------------------------------"
# now move the initial registration template to OUTPUTNAME, otherwise this input gets overwritten.
cp ${REGTEMPLATE} ${TEMPLATE}
fi
if [ ! -s $TEMPLATE ] ; then
echo Your template : $TEMPLATE was not created. This indicates trouble! You may want to check correctness of your input parameters. exiting.
exit
fi
# remove old job bash scripts
rm -f job*.sh
if [ "$RIGID" -eq 1 ] ;
then
count=0
jobIDs=""
RIGID_IMAGESET=""
for IMG in $IMAGESETVARIABLE
do
RIGID_IMAGESET="$RIGID_IMAGESET rigid_${IMG}"
BASENAME=` echo ${IMG} | cut -d '.' -f 1 `
exe=" ${ANTSPATH}/ANTS $DIM -m MI[${TEMPLATE},${IMG},1,32] -o rigid_${IMG} -i 0 --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 $RIGIDTYPE"
exe2="${ANTSPATH}/WarpImageMultiTransform $DIM ${IMG} rigid_${IMG} rigid_${BASENAME}Affine${afftype} -R ${TEMPLATE}"
pexe=" $exe >> job_${count}_metriclog.txt "
qscript="job_${count}_qsub.sh"
rm -f $qscript
if [[ $DOQSUB -eq 5 ]]; then
# SLURM job scripts must start with a shebang
echo '#!/bin/sh' > $qscript
fi
echo "$SCRIPTPREPEND" >> $qscript
echo "$exe" >> $qscript
echo "$exe2" >> $qscript
if [ $DOQSUB -eq 1 ] ; then
id=`qsub -cwd -S /bin/bash -N antsBuildTemplate_rigid -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH $QSUBOPTS $qscript | awk '{print $3}'`
jobIDs="$jobIDs $id"
sleep 0.5
elif [ $DOQSUB -eq 4 ]; then
echo "cp -R /jobtmp/pbstmp.\$PBS_JOBID/* ${currentdir}" >> $qscript;
id=`qsub -N antsrigid -v ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1,LD_LIBRARY_PATH=$LD_LIBRARY_PATH,ANTSPATH=$ANTSPATH $QSUBOPTS -q $DEFQUEUE -l nodes=1:ppn=1 -l walltime=4:00:00 $qscript | awk '{print $1}'`
jobIDs="$jobIDs $id"
sleep 0.5
elif [ $DOQSUB -eq 2 ] ; then
# Send pexe and exe2 to same job file so that they execute in series
echo $pexe >> job${count}_r.sh
echo $exe2 >> job${count}_r.sh
elif [ $DOQSUB -eq 3 ] ; then