Inference cpu Docker container

[akromeo]

I am trying to run the inference cpu docker container however I am running into an issue that it is not setting the BRAIN_MASKING environ variable correctly and therefore not importing brain_extraction function in the image_processing script.

Error: /tmp/zou_2519.log - No such file or directory.
loading nifti files
registration to MNI template space
performing N3 bias correction
performing brain extraction using ANTsPyNet
Traceback (most recent call last):
File "/app/preprocess.py", line 94, in
noelImageProcessor(
File "/app/deepMask/app/utils/image_processing.py", line 440, in pipeline
self.__skull_stripping()
File "/app/deepMask/app/utils/image_processing.py", line 181, in __skull_stripping
prob = brain_extraction(self._t1_n4, modality="t1")
NameError: name 'brain_extraction' is not defined

I am running the Docker image on my Mac OS w M3 processor.

Thanks

[ravnoor]

Could you please fill out the following information, and the actual command executed?

Your Environment

• Version used (e.g. v1.1.1 or commit hash):
• Environment name and version [e.g. Docker (noelmni/deep-fcd:v1.1.2), M1/Intel macOS 14.2.1 with Conda (Python 3.7), Linux (Conda 4.11 w/ Python 3.7)]:
• Hardware (e.g., 4 vCPUs, 16GB RAM, NVIDIA TITAN RTX w/ 24GB VRAM)
• Using GPU or CPU:
• Operating System (OS) and version (if not using the Docker image; e.g. Ubuntu 22.04.4 LTS):
• OS baremetal or virtualized:

[akromeo]

This is the docker command I used except I replaced $PWD w my directory. CA was the subject ID:

$ docker run --rm -it --init --env OMP_NUM_THREADS=6 --volume=$PWD/io:/io noelmni/deep-fcd:latest /app/inference.py CA T1.nii.gz Flair.nii.gz /io cpu 1 1

Not sure what version this is. Version is latest? I don’t know how to tell which docker image version that is pulling.

I am running this on my Mac OS M3 cpu but I am using the docker container which uses ubuntu base image.