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set config for 15 and 17
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@taigw
taigw committed Jan 13, 2018
1 parent ec1af3e commit cf5231a
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Showing 37 changed files with 1,032 additions and 891 deletions.
26 changes: 14 additions & 12 deletions config15/test_all_class.txt
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
[data]
data_root = [/home/guotwang/data/brats_docker_data/pre_process]
data_names = config/test_names.txt
data_root = /home/guotwang/data/BRATS2015_Training
save_folder = result15
data_names = config15/test_names.txt
modality_postfix = [Flair, T1, T1c, T2]
file_postfix = mha

[network1ax]
net_type = MSNet
Expand All @@ -10,7 +12,7 @@ downsample_twice = True
data_shape = [19, 180, 160, 4]
label_shape = [11, 180, 160, 1]
class_num = 2
model_file = model/msnet_wt32_10000.ckpt
model_file = model15/msnet_wt32_10000.ckpt

[network1sg]
net_type = MSNet
Expand All @@ -19,7 +21,7 @@ downsample_twice = True
data_shape = [19, 160, 180, 4]
label_shape = [11, 160, 180, 1]
class_num = 2
model_file = model/msnet_wt32sg_5000.ckpt
model_file = model15/msnet_wt32sg_5000.ckpt

[network1cr]
net_type = MSNet
Expand All @@ -28,7 +30,7 @@ downsample_twice = True
data_shape = [19, 160, 160, 4]
label_shape = [11, 160, 160, 1]
class_num = 2
model_file = model/msnet_wt32cr_5000.ckpt
model_file = model15/msnet_wt32cr_5000.ckpt


[network2ax]
Expand All @@ -38,7 +40,7 @@ downsample_twice = True
data_shape = [19, 96, 96, 4]
label_shape = [11, 96, 96, 1]
class_num = 2
model_file = model/msnet_tc32_20000.ckpt
model_file = model15/msnet_tc32_20000.ckpt

[network2sg]
net_type = MSNet
Expand All @@ -47,7 +49,7 @@ downsample_twice = True
data_shape = [19, 96, 96, 4]
label_shape = [11, 96, 96, 1]
class_num = 2
model_file = model/msnet_tc32sg_5000.ckpt
model_file = model15/msnet_tc32sg_5000.ckpt

[network2cr]
net_type = MSNet
Expand All @@ -56,7 +58,7 @@ downsample_twice = True
data_shape = [19, 96, 96, 4]
label_shape = [11, 96, 96, 1]
class_num = 2
model_file = model/msnet_tc32cr_5000.ckpt
model_file = model15/msnet_tc32cr_5000.ckpt

[network3ax]
net_type = MSNet
Expand All @@ -65,7 +67,7 @@ downsample_twice = False
data_shape = [19, 96, 96, 4]
label_shape = [11, 96, 96, 1]
class_num = 3
model_file = model/msnet_en32_20000.ckpt
model_file = model15/msnet_en32_20000.ckpt

[network3sg]
net_type = MSNet
Expand All @@ -74,7 +76,7 @@ downsample_twice = False
data_shape = [19, 96, 96, 4]
label_shape = [11, 96, 96, 1]
class_num = 3
model_file = model/msnet_en32sg_5000.ckpt
model_file = model15/msnet_en32sg_5000.ckpt

[network3cr]
net_type = MSNet
Expand All @@ -83,8 +85,8 @@ downsample_twice = False
data_shape = [19, 96, 96, 4]
label_shape = [11, 96, 96, 1]
class_num = 3
model_file = model/msnet_en32cr_5000.ckpt
model_file = model15/msnet_en32cr_5000.ckpt

[testing]
test_slice_direction = all
save_folder = result_all

100 changes: 50 additions & 50 deletions config15/test_names.txt
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Original file line number Diff line number Diff line change
@@ -1,50 +1,50 @@
HGG_brats_tcia_pat417_0001
HGG_brats_tcia_pat205_0001
HGG_brats_tcia_pat455_0001
HGG_brats_tcia_pat374_0356
HGG_brats_tcia_pat473_0001
HGG_brats_tcia_pat277_0001
HGG_brats_tcia_pat396_0117
LGG_brats_tcia_pat299_0001
HGG_brats_tcia_pat332_0001
HGG_brats_tcia_pat178_0002
HGG_brats_tcia_pat199_0001
HGG_brats_tcia_pat170_0002
HGG_brats_tcia_pat156_0001
HGG_brats_tcia_pat447_0313
HGG_brats_tcia_pat198_0283
HGG_brats_tcia_pat105_0001
HGG_brats_2013_pat0002_1
HGG_brats_tcia_pat406_0001
LGG_brats_tcia_pat393_0001
HGG_brats_tcia_pat274_0001
LGG_brats_tcia_pat141_0001
HGG_brats_tcia_pat138_0001
LGG_brats_2013_pat0006_1
HGG_brats_tcia_pat314_0001
LGG_brats_2013_pat0014_1
HGG_brats_tcia_pat447_0122
HGG_brats_tcia_pat372_0001
HGG_brats_tcia_pat230_0637
HGG_brats_tcia_pat247_0001
HGG_brats_tcia_pat171_0780
LGG_brats_tcia_pat351_0001
HGG_brats_tcia_pat399_0527
HGG_brats_tcia_pat193_0002
HGG_brats_tcia_pat374_0557
HGG_brats_2013_pat0024_1
HGG_brats_tcia_pat374_0909
HGG_brats_tcia_pat278_0001
HGG_brats_tcia_pat180_0001
HGG_brats_tcia_pat399_0595
HGG_brats_tcia_pat396_0217
HGG_brats_tcia_pat257_0001
HGG_brats_tcia_pat157_0001
HGG_brats_tcia_pat165_0001
HGG_brats_2013_pat0022_1
HGG_brats_tcia_pat444_0001
HGG_brats_tcia_pat399_0002
HGG_brats_tcia_pat399_0156
LGG_brats_tcia_pat428_0001
HGG_brats_tcia_pat171_0950
HGG_brats_tcia_pat399_0479
HGG/brats_tcia_pat417_0001
HGG/brats_tcia_pat205_0001
HGG/brats_tcia_pat455_0001
HGG/brats_tcia_pat374_0356
HGG/brats_tcia_pat473_0001
HGG/brats_tcia_pat277_0001
HGG/brats_tcia_pat396_0117
LGG/brats_tcia_pat299_0001
HGG/brats_tcia_pat332_0001
HGG/brats_tcia_pat178_0002
HGG/brats_tcia_pat199_0001
HGG/brats_tcia_pat170_0002
HGG/brats_tcia_pat156_0001
HGG/brats_tcia_pat447_0313
HGG/brats_tcia_pat198_0283
HGG/brats_tcia_pat105_0001
HGG/brats_2013_pat0002_1
HGG/brats_tcia_pat406_0001
LGG/brats_tcia_pat393_0001
HGG/brats_tcia_pat274_0001
LGG/brats_tcia_pat141_0001
HGG/brats_tcia_pat138_0001
LGG/brats_2013_pat0006_1
HGG/brats_tcia_pat314_0001
LGG/brats_2013_pat0014_1
HGG/brats_tcia_pat447_0122
HGG/brats_tcia_pat372_0001
HGG/brats_tcia_pat230_0637
HGG/brats_tcia_pat247_0001
HGG/brats_tcia_pat171_0780
LGG/brats_tcia_pat351_0001
HGG/brats_tcia_pat399_0527
HGG/brats_tcia_pat193_0002
HGG/brats_tcia_pat374_0557
HGG/brats_2013_pat0024_1
HGG/brats_tcia_pat374_0909
HGG/brats_tcia_pat278_0001
HGG/brats_tcia_pat180_0001
HGG/brats_tcia_pat399_0595
HGG/brats_tcia_pat396_0217
HGG/brats_tcia_pat257_0001
HGG/brats_tcia_pat157_0001
HGG/brats_tcia_pat165_0001
HGG/brats_2013_pat0022_1
HGG/brats_tcia_pat444_0001
HGG/brats_tcia_pat399_0002
HGG/brats_tcia_pat399_0156
LGG/brats_tcia_pat428_0001
HGG/brats_tcia_pat171_0950
HGG/brats_tcia_pat399_0479
14 changes: 8 additions & 6 deletions config15/test_wt.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,9 @@
[data]
data_root = [data/Brats17ValidationData_renamed]
data_names =
data_root = /home/guotwang/data/BRATS2015_Training
save_folder = result15
data_names = config15/test_names.txt
modality_postfix = [Flair, T1, T1c, T2]
file_postfix = mha

[network1ax]
net_type = MSNet
Expand All @@ -9,7 +12,7 @@ downsample_twice = True
data_shape = [19, 180, 160, 4]
label_shape = [11, 180, 160, 1]
class_num = 2
model_file = model_pretrain/msnet_wt32_20000.ckpt
model_file = model15/msnet_wt32_10000.ckpt

[network1sg]
net_type = MSNet
Expand All @@ -18,7 +21,7 @@ downsample_twice = True
data_shape = [19, 160, 180, 4]
label_shape = [11, 160, 180, 1]
class_num = 2
model_file = model_pretrain/msnet_wt32sg_20000.ckpt
model_file = model15/msnet_wt32sg_10000.ckpt

[network1cr]
net_type = MSNet
Expand All @@ -27,9 +30,8 @@ downsample_twice = True
data_shape = [19, 160, 160, 4]
label_shape = [11, 160, 160, 1]
class_num = 2
model_file = model_pretrain/msnet_wt32cr_20000.ckpt
model_file = model15/msnet_wt32cr_10000.ckpt

[testing]
test_slice_direction = all
whole_tumor_only = True
save_folder = results_wt
9 changes: 5 additions & 4 deletions config15/train_en_ax.txt
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
[data]
data_root = [/home/guotwang/data/brats_docker_data/pre_process]
data_names = config/train_names_all_lggx3.txt
data_root = /home/guotwang/data/BRATS2015_Training
data_names = config15/train_names_all_lggx3.txt
modality_postfix = [Flair, T1, T1c, T2]
label_postfix = OT
label_postfix = OT
file_postfix = mha
with_ground_truth = True
batch_size = 5
data_shape = [19, 64, 64, 4]
Expand All @@ -29,4 +30,4 @@ start_iteration = 0
test_iteration = 100
test_step = 10
model_pre_trained =
model_save_prefix = model/msnet_en32
model_save_prefix = model15/msnet_en32
11 changes: 6 additions & 5 deletions config15/train_en_cr.txt
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
[data]
data_root = [/home/guotwang/data/brats_docker_data/pre_process]
data_names = config/train_names_all_lggx3.txt
data_root = /home/guotwang/data/BRATS2015_Training
data_names = config15/train_names_all_lggx3.txt
modality_postfix = [Flair, T1, T1c, T2]
label_postfix = OT
label_postfix = OT
file_postfix = mha
with_ground_truth = True
batch_size = 5
data_shape = [19, 64, 64, 4]
Expand All @@ -28,5 +29,5 @@ snapshot_iteration = 5000
start_iteration = 1
test_iteration = 100
test_step = 10
model_pre_trained = model/msnet_en32cr_init
model_save_prefix = model/msnet_en32cr
model_pre_trained = model15/msnet_en32cr_init
model_save_prefix = model15/msnet_en32cr
11 changes: 6 additions & 5 deletions config15/train_en_sg.txt
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
[data]
data_root = [/home/guotwang/data/brats_docker_data/pre_process]
data_names = config/train_names_all_lggx3.txt
data_root = /home/guotwang/data/BRATS2015_Training
data_names = config15/train_names_all_lggx3.txt
modality_postfix = [Flair, T1, T1c, T2]
label_postfix = OT
label_postfix = OT
file_postfix = mha
with_ground_truth = True
batch_size = 5
data_shape = [19, 64, 64, 4]
Expand All @@ -28,5 +29,5 @@ snapshot_iteration = 5000
start_iteration = 1
test_iteration = 100
test_step = 10
model_pre_trained = model/msnet_en32sg_init
model_save_prefix = model/msnet_en32sg
model_pre_trained = model15/msnet_en32sg_init
model_save_prefix = model15/msnet_en32sg
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