gur9000 / deep_mri_brain_extraction Goto Github PK

$ python deep3Dpredict.py -name OASIS_ISBR_LPBA40__trained_CNN.save -data TCGA-02-0046_1998.11.28_t2.nii.gz -output deep-mask.nii -gridsize 16 

WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.
Using cuDNN version 6021 on context None
Mapped name None to device cuda: GeForce GTX 1080 (0000:01:00.0)
/home/mingrui/anaconda3/envs/p2_3DUnetCNN/lib/python2.7/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
using model-parameters: OASIS_ISBR_LPBA40__trained_CNN.save
loading...
Loaded... 100.0 % (240, 1, 240, 155)  ('TCGA-02-0046_1998.11.28_t2.nii.gz', None)
Total n. of examples: 1 images/volumes
Training on 0 images/volumes
Testing on  1 images/volumes
Building CNN...
Traceback (most recent call last):
  File "deep3Dpredict.py", line 200, in <module>
    main()
  File "deep3Dpredict.py", line 194, in main
    network_size_factor = float(args.CNN_width_scale))
  File "deep3Dpredict.py", line 116, in predict
    auto_threshold_labels = auto_threshold_labels)
  File "/mnt/960EVO/workspace/Deep_MRI_brain_extraction/utils/Segmentation_trainer.py", line 232, in Build3D
    dense_output_from_fragments = is_last_layer and use_fragment_pooling)
  File "/mnt/960EVO/workspace/Deep_MRI_brain_extraction/NNet_Core/NN_ConvNet.py", line 350, in addConvLayer
    output_stride = self.output_stride, verbose = self.verbose)
  File "/mnt/960EVO/workspace/Deep_MRI_brain_extraction/NNet_Core/NN_ConvLayer_3D.py", line 271, in __init__
    output_shape = list(  theano.function([input], self.output.shape, mode = self.mode)(numpy.zeros((1 if input_shape[0]==None else input_shape[0],)+input_shape[1:],dtype=numpy.float32)))
  File "/home/mingrui/anaconda3/envs/p2_3DUnetCNN/lib/python2.7/site-packages/theano/compile/function_module.py", line 917, in __call__
    storage_map=getattr(self.fn, 'storage_map', None))
  File "/home/mingrui/anaconda3/envs/p2_3DUnetCNN/lib/python2.7/site-packages/theano/gof/link.py", line 325, in raise_with_op
    reraise(exc_type, exc_value, exc_trace)
  File "/home/mingrui/anaconda3/envs/p2_3DUnetCNN/lib/python2.7/site-packages/theano/compile/function_module.py", line 903, in __call__
    self.fn() if output_subset is None else\
RuntimeError: error getting worksize: CUDNN_STATUS_BAD_PARAM
Apply node that caused the error: GpuDnnConv{algo='small', inplace=True, num_groups=1}(GpuContiguous.0, GpuContiguous.0, GpuAllocEmpty{dtype='float32', context_name=None}.0, GpuDnnConvDesc{border_mode='valid', subsample=(1, 1), dilation=(1, 1), conv_mode='conv', precision='float32', num_groups=1}.0, Constant{1.0}, Constant{0.0})
Toposort index: 26
Inputs types: [GpuArrayType<None>(float32, (False, True, False, False)), GpuArrayType<None>(float32, (False, True, False, False)), GpuArrayType<None>(float32, 4D), <theano.gof.type.CDataType object at 0x7ff807861bd0>, Scalar(float32), Scalar(float32)]
Inputs shapes: [(83, 1, 83, 83), (64, 1, 4, 4), (83, 64, 80, 80), 'No shapes', (), ()]
Inputs strides: [(27556, 27556, 332, 4), (64, 64, 16, 4), (1638400, 25600, 320, 4), 'No strides', (), ()]
Inputs values: ['not shown', 'not shown', 'not shown', <capsule object NULL at 0x7ff8079ad900>, 1.0, 0.0]
Outputs clients: [[GpuReshape{5}(GpuDnnConv{algo='small', inplace=True, num_groups=1}.0, TensorConstant{[83 16  4 80 80]})]]

Backtrace when the node is created(use Theano flag traceback.limit=N to make it longer):
  File "deep3Dpredict.py", line 200, in <module>
    main()
  File "deep3Dpredict.py", line 194, in main
    network_size_factor = float(args.CNN_width_scale))
  File "deep3Dpredict.py", line 116, in predict
    auto_threshold_labels = auto_threshold_labels)
  File "/mnt/960EVO/workspace/Deep_MRI_brain_extraction/utils/Segmentation_trainer.py", line 232, in Build3D
    dense_output_from_fragments = is_last_layer and use_fragment_pooling)
  File "/mnt/960EVO/workspace/Deep_MRI_brain_extraction/NNet_Core/NN_ConvNet.py", line 350, in addConvLayer
    output_stride = self.output_stride, verbose = self.verbose)
  File "/mnt/960EVO/workspace/Deep_MRI_brain_extraction/NNet_Core/NN_ConvLayer_3D.py", line 217, in __init__
    filters_shape=filter_shape, signals_shape = input_shape if input_shape[0]!=None else None

HINT: Use the Theano flag 'exception_verbosity=high' for a debugprint and storage map footprint of this apply node.

python Deep_MRI_brain_extraction/deep3Dpredict.py -n Deep_MRI_brain_extraction/OASIS_ISBR_LPBA40__trained_CNN.save -i  $target -gridsize 16
ValueError: The provided save file/directory does not contain any saved model (file ending in .save)

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