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taigw / brats17

Brain tumor segmentation for MICCAI 2017 BraTS challenge
BSD 3-Clause "New" or "Revised" License
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net1 output is null #31

Open Gaojun211 opened 5 years ago

Gaojun211 commented 5 years ago

When I test the model,it occurs a problem.The situation is as follows： customer@node01:~/FCN/brats17-master$ python test.py test_all_class.txt data data_root /home/customer/data/Brats17ValidationData /home/customer/data/Brats17ValidationData data save_folder /home/customer/data/result17/two /home/customer/data/result17/two data data_names config17/test_names_temp.txt config17/test_names_temp.txt data modality_postfix [flair, t1, t1ce, t2] ['flair', 't1', 't1ce', 't2'] data file_postfix nii.gz nii.gz network1ax net_type MSNet MSNet network1ax net_name MSNet_WT32 MSNet_WT32 network1ax downsample_twice True True network1ax data_shape [19, 180, 160, 4] [19, 180, 160, 4] network1ax label_shape [11, 180, 160, 1] [11, 180, 160, 1] network1ax class_num 2 2 network1ax model_file model17/msnet_wt32_20000.ckpt model17/msnet_wt32_20000.ckpt network1sg net_type MSNet MSNet network1sg net_name MSNet_WT32sg MSNet_WT32sg network1sg downsample_twice True True network1sg data_shape [19, 160, 180, 4] [19, 160, 180, 4] network1sg label_shape [11, 160, 180, 1] [11, 160, 180, 1] network1sg class_num 2 2 network1sg model_file model17/msnet_wt32sg_20000.ckpt model17/msnet_wt32sg_20000.ckpt network1cr net_type MSNet MSNet network1cr net_name MSNet_WT32cr MSNet_WT32cr network1cr downsample_twice True True network1cr data_shape [19, 160, 160, 4] [19, 160, 160, 4] network1cr label_shape [11, 160, 160, 1] [11, 160, 160, 1] network1cr class_num 2 2 network1cr model_file model17/msnet_wt32cr_20000.ckpt model17/msnet_wt32cr_20000.ckpt network2ax net_type MSNet MSNet network2ax net_name MSNet_TC32 MSNet_TC32 network2ax downsample_twice True True network2ax data_shape [19, 96, 96, 4] [19, 96, 96, 4] network2ax label_shape [11, 96, 96, 1] [11, 96, 96, 1] network2ax class_num 2 2 network2ax model_file model17/msnet_tc32_20000.ckpt model17/msnet_tc32_20000.ckpt network2sg net_type MSNet MSNet network2sg net_name MSNet_TC32sg MSNet_TC32sg network2sg downsample_twice True True network2sg data_shape [19, 96, 96, 4] [19, 96, 96, 4] network2sg label_shape [11, 96, 96, 1] [11, 96, 96, 1] network2sg class_num 2 2 network2sg model_file model17/msnet_tc32sg_20000.ckpt model17/msnet_tc32sg_20000.ckpt network2cr net_type MSNet MSNet network2cr net_name MSNet_TC32cr MSNet_TC32cr network2cr downsample_twice True True network2cr data_shape [19, 96, 96, 4] [19, 96, 96, 4] network2cr label_shape [11, 96, 96, 1] [11, 96, 96, 1] network2cr class_num 2 2 network2cr model_file model17/msnet_tc32cr_20000.ckpt model17/msnet_tc32cr_20000.ckpt network3ax net_type MSNet MSNet network3ax net_name MSNet_EN32 MSNet_EN32 network3ax downsample_twice False False network3ax data_shape [19, 96, 96, 4] [19, 96, 96, 4] network3ax label_shape [11, 96, 96, 1] [11, 96, 96, 1] network3ax class_num 2 2 network3ax model_file model17/msnet_en32_20000.ckpt model17/msnet_en32_20000.ckpt network3sg net_type MSNet MSNet network3sg net_name MSNet_EN32sg MSNet_EN32sg network3sg downsample_twice False False network3sg data_shape [19, 96, 96, 4] [19, 96, 96, 4] network3sg label_shape [11, 96, 96, 1] [11, 96, 96, 1] network3sg class_num 2 2 network3sg model_file model17/msnet_en32sg_20000.ckpt model17/msnet_en32sg_20000.ckpt network3cr net_type MSNet MSNet network3cr net_name MSNet_EN32cr MSNet_EN32cr network3cr downsample_twice False False network3cr data_shape [19, 96, 96, 4] [19, 96, 96, 4] network3cr label_shape [11, 96, 96, 1] [11, 96, 96, 1] network3cr class_num 2 2 network3cr model_file model17/msnet_en32cr_20000.ckpt model17/msnet_en32cr_20000.ckpt testing test_slice_direction all all 2019-03-07 16:12:09.919758: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2019-03-07 16:12:10.170770: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1212] Found device 0 with properties: name: TITAN Xp major: 6 minor: 1 memoryClockRate(GHz): 1.582 pciBusID: 0000:02:00.0 totalMemory: 11.90GiB freeMemory: 11.46GiB 2019-03-07 16:12:10.344403: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1212] Found device 1 with properties: name: TITAN Xp major: 6 minor: 1 memoryClockRate(GHz): 1.582 pciBusID: 0000:81:00.0 totalMemory: 11.90GiB freeMemory: 11.74GiB 2019-03-07 16:12:10.344474: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1227] Device peer to peer matrix 2019-03-07 16:12:10.344503: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1233] DMA: 0 1 2019-03-07 16:12:10.344512: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1243] 0: Y N 2019-03-07 16:12:10.344518: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1243] 1: N Y 2019-03-07 16:12:10.344528: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1312] Adding visible gpu devices: 0, 1 2019-03-07 16:12:10.844580: I tensorflow/core/common_runtime/gpu/gpu_device.cc:993] Creating TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 11101 MB memory) -> physical GPU (device: 0, name: TITAN Xp, pci bus id: 0000:02:00.0, compute capability: 6.1) 2019-03-07 16:12:10.845693: I tensorflow/core/common_runtime/gpu/gpu_device.cc:993] Creating TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:1 with 11364 MB memory) -> physical GPU (device: 1, name: TITAN Xp, pci bus id: 0000:81:00.0, compute capability: 6.1) INFO:niftynet: Restoring parameters from model17/msnet_wt32_20000.ckpt INFO:niftynet: Restoring parameters from model17/msnet_wt32sg_20000.ckpt INFO:niftynet: Restoring parameters from model17/msnet_wt32cr_20000.ckpt INFO:niftynet: Restoring parameters from model17/msnet_tc32_20000.ckpt INFO:niftynet: Restoring parameters from model17/msnet_tc32sg_20000.ckpt INFO:niftynet: Restoring parameters from model17/msnet_tc32cr_20000.ckpt INFO:niftynet: Restoring parameters from model17/msnet_en32_20000.ckpt INFO:niftynet: Restoring parameters from model17/msnet_en32sg_20000.ckpt INFO:niftynet: Restoring parameters from model17/msnet_en32cr_20000.ckpt Data load, 100.0% finished net1 output is null Brats17_TCIA_600_1 Brats17_TCIA_600_1 test time 34.72197985649109

and when I open the Brats17_TCIA_600_1.nii.gz using mipav ,it's whole black.And I changed the code of test_all_class as follows: data_root = /home/customer/data/Brats17ValidationData save_folder = /home/customer/data/result17/two all the folder are exist.Could you please suggest the solution.

russchua commented 4 years ago

Hi @Gaojun211 and @taigw,

Have you found a solution to this?

I have a similar error: /content/brats17/util/data_process.py:95: RuntimeWarning: divide by zero encountered in true_divide out = (volume - mean)/std /content/brats17/util/data_process.py:95: RuntimeWarning: invalid value encountered in true_divide out = (volume - mean)/std Data load, 100.0% finished 2019-10-31 01:47:45.793500: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcudnn.so.7 2019-10-31 01:47:48.677996: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcublas.so.10.0 net1 output is null HGG/Brats17_CBICA_ATX_1 HGG/Brats17_CBICA_ATX_1 net1 output is null HGG/Brats17_CBICA_AXN_1 HGG/Brats17_CBICA_AXN_1 test time 86.31490552425385