Run the Docker and singularity file on HPC

[lyhoo23618-csu]

Hello everyone,

I am trying to run this great toolbox on HPC. So i used apptainer to build a sif image from the corresponding docker container (jqmcginnis/lst-ai:latest). Afterwards, i run this sif image using apptainer in my cluster. However, it failed in the middle. And the log file showed: ... running postprocessing... exporting segmentation... Limiting the number of threads to 64 Limiting the number of threads to 64 Running LST Segmentation. Running segmentation on /GPU:0. Running model 0. /usr/local/lib/python3.10/dist-packages/keras/src/layers/activations/leaky_relu.py:41: UserWarning: Argument alpha is deprecated. Use negative_slope instead. warnings.warn( Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/keras/src/ops/operation.py", line 234, in from_config return cls(**config) File "/usr/local/lib/python3.10/dist-packages/keras/src/layers/convolutional/conv3d_transpose.py", line 120, in init super().init( File "/usr/local/lib/python3.10/dist-packages/keras/src/layers/convolutional/base_conv_transpose.py", line 94, in init super().init( File "/usr/local/lib/python3.10/dist-packages/keras/src/layers/layer.py", line 266, in init raise ValueError( ValueError: Unrecognized keyword arguments passed to Conv3DTranspose: {'groups': 1}

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/local/bin/lst", line 7, in exec(compile(f.read(), file, 'exec')) File "/custom_apps/lst_directory/LST-AI/LST_AI/lst", line 320, in unet_segmentation(mni_t1=path_mni_stripped_t1w, File "/custom_apps/lst_directory/LST-AI/LST_AI/segment.py", line 102, in unet_segmentation mdl = load_custom_model(model, compile=False) File "/custom_apps/lst_directory/LST-AI/LST_AI/custom_tf.py", line 28, in load_custom_model return tf.keras.models.load_model(model_path, custom_objects=custom_objects, compile=compile) File "/usr/local/lib/python3.10/dist-packages/keras/src/saving/saving_api.py", line 189, in load_model return legacy_h5_format.load_model_from_hdf5( File "/usr/local/lib/python3.10/dist-packages/keras/src/legacy/saving/legacy_h5_format.py", line 133, in load_model_from_hdf5 model = saving_utils.model_from_config( File "/usr/local/lib/python3.10/dist-packages/keras/src/legacy/saving/saving_utils.py", line 85, in model_from_config return serialization.deserialize_keras_object( File "/usr/local/lib/python3.10/dist-packages/keras/src/legacy/saving/serialization.py", line 495, in deserialize_keras_object deserialized_obj = cls.from_config( File "/usr/local/lib/python3.10/dist-packages/keras/src/models/model.py", line 521, in from_config return functional_from_config( File "/usr/local/lib/python3.10/dist-packages/keras/src/models/functional.py", line 477, in functional_from_config process_layer(layer_data) File "/usr/local/lib/python3.10/dist-packages/keras/src/models/functional.py", line 457, in process_layer layer = saving_utils.model_from_config( File "/usr/local/lib/python3.10/dist-packages/keras/src/legacy/saving/saving_utils.py", line 85, in model_from_config return serialization.deserialize_keras_object( File "/usr/local/lib/python3.10/dist-packages/keras/src/legacy/saving/serialization.py", line 504, in deserialize_keras_object deserialized_obj = cls.from_config(cls_config) File "/usr/local/lib/python3.10/dist-packages/keras/src/ops/operation.py", line 236, in from_config raise TypeError( TypeError: Error when deserializing class 'Conv3DTranspose' using config={'name': 'conv3d_transpose', 'trainable': True, 'dtype': 'float32', 'filters': 140, 'kernel_size': [4, 4, 4], 'strides': [2, 2, 2], 'padding': 'same', 'data_format': 'channels_last', 'groups': 1, 'activation': 'linear', 'use_bias': False, 'kernel_initializer': {'class_name': 'HeUniform', 'config': {'seed': None}}, 'bias_initializer': {'class_name': 'Zeros', 'config': {}}, 'kernel_regularizer': None, 'bias_regularizer': None, 'activity_regularizer': None, 'kernel_constraint': None, 'bias_constraint': None, 'output_padding': None}.

Exception encountered: Unrecognized keyword arguments passed to Conv3DTranspose: {'groups': 1}

Any help or guidance would be greatly appreciated.

Hao

[jqmcginnis]

@lyhoo23618-csu, I will look into this and report back.

However, in the meantime, I would like to disclose that @darkstorm4hack is not a maintainer of this repository. Additionally, I am unsure which file the links posted by @darkstorm4hack are directing us to, as there is no description and the same link has been posted three times. Please be careful!

[lyhoo23618-csu]

Hi, here’s an update. I found that the Singularity file (SIF) built from the CPU version of the Docker container (docker pull jqmcginnis/lst-ai_cpu) works well.

However, I’m a bit confused about the annotation file. Based on the publications of this tool, I understood that label 1 represents periventricular (PV), label 2 is for juxtacortical, label 3 is for subcortical, and label 4 is for infratentorial. In the output of my segmentation, lesions located in both the periventricular and subcortical regions are labeled as 2 (green in the figure), while part of the subcortical region is marked as label 3 (blue in the figure). Did I misunderstand the meaning of these labels?