sergivalverde
commented
5 years ago Hi, If you are using the docker, then you don't have to install anything apart from docker and be sure that the machine running the code has the proper nvidia-drivers and cuda. I would encourage to use this version of nicmslesions:
Then go to nicmslesions and follow the instructions. It's basically using a docker file from the Docker hub and running everything from a shell script. We have this version running in several machines without problems.
Let met know, s
zswgzx
I'm trying to perform inference using the pre-trained model, but have the following error.
configuration options:
modalities : ['FLAIR', 'T1'] fract_negative_positive : 2.0 test_folder : /path/to/testing weight_paths : None load_weights : True t_bin : 0.5 min_error : 0.5 num_layers : None max_epochs : 400 pretrained_model : baseline_2ch image_tags : ['flair', 't1'] gpu_number : 2 denoise_iter : 3 roi_tags : ['lesion'] register_modalities : True save_tmp : True denoise : True output_folder : /output experiment : baseline_2ch mod3_tags : ['None'] t1_tags : ['t1'] batch_size : 128 x_names : ['FLAIR_brain.nii.gz', 'T1_brain.nii.gz'] current_scan : scan full_train : False train_folder : /path/to/training mod4_tags : ['None'] skull_stripping : True net_verbose : 1 patience : 50 flair_tags : ['flair'] patch_size : (11, 11, 11) balanced_training : False l_min : 10 out_name : out_seg.nii.gz min_th : 0.5 debug : True randomize_train : True train_split : 0.25 pretrained : None fully_convolutional : False
DEBUG: 2 Using TensorFlow backend. Traceback (most recent call last): File "nic_infer_segmentation_batch.py", line 97, in
model = cascade_model(options)
File "/home/docker/src/libs/CNN/build_model.py", line 95, in cascade_model
model = get_network(options)
File "/home/docker/src/libs/CNN/nets.py", line 24, in get_network
net_input = Input(name='in1', shape=(channels,) + options['patch_size'])
File "/miniconda/lib/python2.7/site-packages/keras/engine/topology.py", line 1375, in Input
input_tensor=tensor)
File "/miniconda/lib/python2.7/site-packages/keras/engine/topology.py", line 1286, in init
name=self.name)
File "/miniconda/lib/python2.7/site-packages/keras/backend/tensorflow_backend.py", line 349, in placeholder
x = tf.placeholder(dtype, shape=shape, name=name)
AttributeError: 'module' object has no attribute 'placeholder'
docker@19764b608857:~/src$ ls init.py config nets utils app.py libs nic_infer_segmentation_batch.py cnn_scripts.py logonic.png nic_train_network_batch.py
GPU is completely new to me, so any help would be appreciated.