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Deep-MI / FatSegNet

Deep CNN for Abdominal Adipose Tissue Segmentation on Dixon MRI
Apache License 2.0
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Error in running FatSegNet implementation using CPU docker #8

Closed ValeBra93 closed 3 years ago

ValeBra93 commented 4 years ago

Hi everyone, I am trying to run FatSegNet implementation using CPU compatible docker image using the following command:

docker run -it --rm --name fatsegnet -u $(id -u) -v /mnt/NAS_249/Processing/Brancato/FatSegNet/my_dataset/:/tool/Data -v /mnt/NAS_249/Processing/Brancato/FatSegNet/my_dataset_output/:/tool/Output adipose_tool:cpu_v1

However, this command doesn't work and the following message appears: /usr/local/lib/python3.5/dist-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 TensorFlow backend.

I cannot find where is the error. I am trying to test FatSegNet using the same data for the three subject and organizing the dataset as follows: image image

Although mount the main data directory my_dataset to /tool/Data and the desire local output folder to /tool/Output, any files appear in my_dataset_output folder and the processing seems not to start. image

Please, could someone help me? Thanks in advance!!

ValeBra93 commented 4 years ago

I would point out that, when running the reported command (docker run -it --rm --name fatsegnet -u $(id -u) -v /mnt/NAS_249/Processing/Brancato/FatSegNet/my_dataset/:/tool/Data -v /mnt/NAS_249/Processing/Brancato/FatSegNet/my_dataset_output/:/tool/Output adipose_tool:cpu_v1), the folder my_dataset_output appears, but it results empty!