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merge_structures.sh
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#!/bin/bash
#Passing the variables from command line
data_pat="/data/processed/nrrd"
outputname="GTV.nrrd"
input_roi1="GTVp1.nrrd"
input_roi2="GTVnsum.nrrd"
declare -a excluded_patients_GTVp1=("P0484C0006I13347712" "P0484C0006I13348105" "P0484C0006I13349751" "P0484C0006I13352429" "P0484C0006I13353173" "P0484C0006I13358312" "P0484C0006I13359183" "P0484C0006I13362784" "P0484C0006I13363429" "P0484C0006I13364175" "P0484C0006I13365895" "P0484C0006I13366119" "P0484C0006I13369845" "P0484C0006I1902800" "P0484C0006I3078632" "P0484C0006I4221336" "P0484C0006I5394488" "P0484C0006I5822367" "P0484C0006I59369" "P0484C0006I6553728" "P0484C0006I7903295" "P0484C0006I8868250")
declare -a excluded_patients_GTVnsum=("P0484C0006I13347331" "P0484C0006I13347539" "P0484C0006I13349927" "P0484C0006I13351656" "P0484C0006I13352562" "P0484C0006I13352595" "P0484C0006I13352907" "P0484C0006I13354939" "P0484C0006I13354987" "P0484C0006I13355627" "P0484C0006I13356256" "P0484C0006I13357020" "P0484C0006I13357957" "P0484C0006I13362687" "P0484C0006I13365669" "P0484C0006I13366348" "P0484C0006I13366557" "P0484C0006I13367199" "P0484C0006I13367213" "P0484C0006I13367610" "P0484C0006I13368733" "P0484C0006I13369197" "P0484C0006I1464723" "P0484C0006I18991" "P0484C0006I400173" "P0484C0006I4727106" "P0484C0006I5877329" "P0484C0006I6960259" "P0484C0006I7964928" "P0484C0006I8108763")
declare -a included_patients=(P0484C0006I18991
P0484C0006I59369
P0484C0006I164615
P0484C0006I255973
P0484C0006I286527
P0484C0006I288238
P0484C0006I351311
P0484C0006I400173
P0484C0006I466444
P0484C0006I535883
P0484C0006I643251
P0484C0006I655943
P0484C0006I734905
P0484C0006I807046
P0484C0006I870836
P0484C0006I939188
P0484C0006I957811
P0484C0006I1025258
P0484C0006I1066288
P0484C0006I1127942
P0484C0006I1178272
P0484C0006I1210294
P0484C0006I1440007
P0484C0006I1464723
P0484C0006I1466342
P0484C0006I1486185
P0484C0006I1505846
P0484C0006I1638206
P0484C0006I1728095
P0484C0006I1751485
P0484C0006I1902800
P0484C0006I1914751
P0484C0006I2137448
P0484C0006I2247602
P0484C0006I2263367
P0484C0006I2425633
P0484C0006I2463795
P0484C0006I2478924
P0484C0006I2538235
P0484C0006I2670581
P0484C0006I2739827
P0484C0006I2830787
P0484C0006I2861049
P0484C0006I3059728
P0484C0006I3078632
P0484C0006I3136723
P0484C0006I3216784
P0484C0006I3329101
P0484C0006I3839740
P0484C0006I3888567
P0484C0006I4133203
P0484C0006I4221336
P0484C0006I4336830
P0484C0006I4511940
P0484C0006I4666481
P0484C0006I4699095
P0484C0006I4727106
P0484C0006I4879060
P0484C0006I4898034
P0484C0006I4920805
P0484C0006I5294029
P0484C0006I5341380
P0484C0006I5394488
P0484C0006I5509583
P0484C0006I5545446
P0484C0006I5822367
P0484C0006I5877329
P0484C0006I5905039
P0484C0006I5953204
P0484C0006I6128191
P0484C0006I6514379
P0484C0006I6553728
P0484C0006I6671568
P0484C0006I6742969
P0484C0006I6750743
P0484C0006I6776206
P0484C0006I6821160
P0484C0006I6845732
P0484C0006I6960259
P0484C0006I7132926
P0484C0006I7140821
P0484C0006I7149120
P0484C0006I7221995
P0484C0006I7534100
P0484C0006I7742201
P0484C0006I7775387
P0484C0006I7799273
P0484C0006I7903295
P0484C0006I7942550
P0484C0006I7964928
P0484C0006I8108763
P0484C0006I8228649
P0484C0006I8288698
P0484C0006I8505289
P0484C0006I8523840
P0484C0006I8549533
P0484C0006I8615025
P0484C0006I8755777
P0484C0006I8798032
P0484C0006I8842777
P0484C0006I8846971
P0484C0006I8847939
P0484C0006I8868250
P0484C0006I9170972
P0484C0006I9182550
P0484C0006I9216593
P0484C0006I9290290
P0484C0006I9390150
P0484C0006I9448529
P0484C0006I9573705
P0484C0006I9584506
P0484C0006I9719208
P0484C0006I9771899
P0484C0006I9774388
P0484C0006I9810940
P0484C0006I9875819
P0484C0006I9973944
P0484C0006I13345805
P0484C0006I13346199
P0484C0006I13346424
P0484C0006I13347331
P0484C0006I13347407
P0484C0006I13347539
P0484C0006I13347594
P0484C0006I13347712
P0484C0006I13347800
P0484C0006I13348105
P0484C0006I13348555
P0484C0006I13348763
P0484C0006I13348872
P0484C0006I13349066
P0484C0006I13349113
P0484C0006I13349332
P0484C0006I13349468
P0484C0006I13349491
P0484C0006I13349622
P0484C0006I13349624
P0484C0006I13349751
P0484C0006I13349852
P0484C0006I13349927
P0484C0006I13350074
P0484C0006I13350375
P0484C0006I13350742
P0484C0006I13350782
P0484C0006I13350952
P0484C0006I13351291
P0484C0006I13351366
P0484C0006I13351420
P0484C0006I13351656
P0484C0006I13351787
P0484C0006I13352100
P0484C0006I13352359
P0484C0006I13352398
P0484C0006I13352429
P0484C0006I13352557
P0484C0006I13352562
P0484C0006I13352595
P0484C0006I13352637
P0484C0006I13352698
P0484C0006I13352804
P0484C0006I13352894
P0484C0006I13352907
P0484C0006I13353045
P0484C0006I13353067
P0484C0006I13353137
P0484C0006I13353140
P0484C0006I13353173
P0484C0006I13353183
P0484C0006I13353374
P0484C0006I13353646
P0484C0006I13353684
P0484C0006I13353764
P0484C0006I13353887
P0484C0006I13353924
P0484C0006I13353967
P0484C0006I13354409
P0484C0006I13354465
P0484C0006I13354570
P0484C0006I13354845
P0484C0006I13354939
P0484C0006I13354987
P0484C0006I13355135
P0484C0006I13355148
P0484C0006I13355155
P0484C0006I13355203
P0484C0006I13355627
P0484C0006I13355703
P0484C0006I13355798
P0484C0006I13355836
P0484C0006I13355988
P0484C0006I13356149
P0484C0006I13356226
P0484C0006I13356256
P0484C0006I13356948
P0484C0006I13357020
P0484C0006I13357128
P0484C0006I13357481
P0484C0006I13357582
P0484C0006I13357620
P0484C0006I13357819
P0484C0006I13357861
P0484C0006I13357957
P0484C0006I13358219
P0484C0006I13358312
P0484C0006I13358457
P0484C0006I13358522
P0484C0006I13358535
P0484C0006I13358675
P0484C0006I13358848
P0484C0006I13359183
P0484C0006I13359512
P0484C0006I13359661
P0484C0006I13359714
P0484C0006I13359886
P0484C0006I13359979
P0484C0006I13360075
P0484C0006I13360079
P0484C0006I13360122
P0484C0006I13360174
P0484C0006I13360400
P0484C0006I13360597
P0484C0006I13360600
P0484C0006I13360678
P0484C0006I13360752
P0484C0006I13360959
P0484C0006I13361041
P0484C0006I13361214
P0484C0006I13361535
P0484C0006I13361624
P0484C0006I13361722
P0484C0006I13361792
P0484C0006I13362113
P0484C0006I13362273
P0484C0006I13362275
P0484C0006I13362282
P0484C0006I13362283
P0484C0006I13362402
P0484C0006I13362687
P0484C0006I13362784
P0484C0006I13362852
P0484C0006I13362855
P0484C0006I13363156
P0484C0006I13363429
P0484C0006I13363520
P0484C0006I13363562
P0484C0006I13363666
P0484C0006I13363979
P0484C0006I13364049
P0484C0006I13364175
P0484C0006I13364267
P0484C0006I13364395
P0484C0006I13364611
P0484C0006I13364614
P0484C0006I13364655
P0484C0006I13364872
P0484C0006I13364927
P0484C0006I13365585
P0484C0006I13365668
P0484C0006I13365669
P0484C0006I13365737
P0484C0006I13365779
P0484C0006I13365895
P0484C0006I13365926
P0484C0006I13365927
P0484C0006I13365971
P0484C0006I13366119
P0484C0006I13366254
P0484C0006I13366348
P0484C0006I13366557
P0484C0006I13366606
P0484C0006I13366607
P0484C0006I13366614
P0484C0006I13366790
P0484C0006I13366991
P0484C0006I13367199
P0484C0006I13367213
P0484C0006I13367533
P0484C0006I13367538
P0484C0006I13367565
P0484C0006I13367609
P0484C0006I13367610
P0484C0006I13367923
P0484C0006I13367924
P0484C0006I13368195
P0484C0006I13368237
P0484C0006I13368391
P0484C0006I13368543
P0484C0006I13368733
P0484C0006I13368795
P0484C0006I13368798
P0484C0006I13369197
P0484C0006I13369845
P0484C0006I13369967
P0484C0006I13369969
P0484C0006I13370113
P0484C0006I13370540)
for pat in ${excluded_patients_GTVp1[@]}; do
echo $data_pat/$pat/rt_binarymasks/$outputname
#echo $data_pat/$pat/rt_binarymasks/$input_roi1
echo $data_pat/$pat/rt_binarymasks/$input_roi2
plastimatch add --output $data_pat/$pat/rt_binarymasks/$outputname $data_pat/$pat/rt_binarymasks/$input_roi2 #$data_pat/$pat/rt_binarymasks/$input_roi2
done