AICONSlab / AICONSlab/HyperMapp3r
Error during WMH segmentation in HyperMapp3r
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Beschreibung
Dear experts,
First of all, thank you for this tool and making your pre-trained models publicly available. I tried to conduct the WMH segmentation in one subject using a T1w and a FLAIR image of one subject using the HyperMapp3r GUI. However, I received the following warnings and errors.
Could you help me to solve this issue?.
Thank you very much in advance.
Using TensorFlow backend.
QPixmap::scaled: Pixmap is a null pixmap
Using TensorFlow backend.
t1w path: /home/usuario/Escritorio/try/t1_4189.nii
flair path: /home/usuario/Escritorio/try/mrfl_4189.nii
mask path:
mask path:
mask path: /home/usuario/Escritorio/try/brainmask_4189.nii
running HyperMapp3r with the following command:
hypermapper seg_wmh --t1w /home/usuario/Escritorio/try/t1_4189.nii --flair /home/usuario/Escritorio/try/mrfl_4189.nii --mask /home/usuario/Escritorio/try/brainmask_4189.nii
Using TensorFlow backend.
input subject: try
pre-processing.......
Warning: input image is not in RPI or LPI orientation..
re-orienting image to standard orientation based on orient tags (please make sure they are correct)
LPI
Warning: input image is not in RPI or LPI orientation..
re-orienting image to standard orientation based on orient tags (please make sure they are correct)
LPI
pre-processing t1_4189
skull stripping ...
cropping ...
standardization ...
mean is:962.13794
std is:315.2472
pre-processing mrfl_4189
Warning: input image is not in RPI or LPI orientation..
re-orienting image to standard orientation based on orient tags (please make sure they are correct)
LPI
skull stripping ...
cropping ...
standardization ...
mean is:989.2982
std is:353.02637
resmapling ...
resmapling ...
predicting WMH segmentation using MC Dropout with 20 samples
0
loading pre-trained model
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:497: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3636: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:228: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:159: The name tf.get_default_session is deprecated. Please use tf.compat.v1.get_default_session instead.
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:164: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:169: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:173: The name tf.global_variables is deprecated. Please use tf.compat.v1.global_variables instead.
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:182: The name tf.is_variable_initialized is deprecated. Please use tf.compat.v1.is_variable_initialized instead.
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:189: The name tf.variables_initializer is deprecated. Please use tf.compat.v1.variables_initializer instead.
WARNING:tensorflow:From /home/usuario/anaconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3019: calling dropout (from tensorflow.python.ops.nn_ops) with keep_prob is deprecated and will be removed in a future version.
Instructions for updating:
Please use `rate` instead of `keep_prob`. Rate should be set to `rate = 1 - keep_prob`.
Traceback (most recent call last):
File "/home/usuario/anaconda3/bin/hypermapper", line 33, in
sys.exit(load_entry_point('HyperMapp3r', 'console_scripts', 'hypermapper')())
File "/home/usuario/HyperMapp3r/hypermapper/cli.py", line 164, in main
args.func(args)
File "/home/usuario/HyperMapp3r/hypermapper/cli.py", line 37, in run_hypermapper
hypermapper.main(args)
File "/home/usuario/HyperMapp3r/hypermapper/segment/hypermapper.py", line 384, in main
affine=res.affine, output_label_map=True, labels=1)
File "/home/usuario/HyperMapp3r/hypermapper/deep/predict.py", line 91, in run_test_case
model.load_weights(model_weights)
File "/home/usuario/anaconda3/lib/python3.7/site-packages/keras/engine/topology.py", line 2622, in load_weights
load_weights_from_hdf5_group(f, self.layers)
File "/home/usuario/anaconda3/lib/python3.7/site-packages/keras/engine/topology.py", line 3090, in load_weights_from_hdf5_group
original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'
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