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Updates aide-svrtk MAP with MONAI-based CNN #13

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Updates aide-svrtk MAP with MONAI-based CNN #13

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65e02cb
monai auto-proc-svrtk update
alenauus Sep 11, 2023
4b90fb9
monai auto-proc-svrtk update
alenauus Sep 11, 2023
5572cf4
log message update
alenauus Sep 12, 2023
628a93c
bash script update
alenauus Sep 12, 2023
1c8d3f7
updated docker files with software paths
alenauus Sep 22, 2023
691d563
script path and version updates
alenauus Sep 28, 2023
f44dc9d
updated file paths
alenauus Oct 1, 2023
451c02e
map version update
alenauus Oct 1, 2023
c76b8e6
updated docker file
alenauus Oct 1, 2023
7440546
Merge branch '10-monai-brain-3d-pipeline' of https://github.com/SVRTK…
alenauus Oct 1, 2023
2c6f200
updated description with auto-proc-svrtk ref.
alenauus Oct 1, 2023
cd69bfe
Updates Clinical Workflow file to reflect v0.2.1
tomaroberts Oct 12, 2023
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28 changes: 14 additions & 14 deletions app/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ WORKDIR /var/monai

# Add SVRTK to MAP

WORKDIR /home
WORKDIR /bin

# Install general libraries
RUN apt-get update && apt-get install --no-install-recommends --no-install-suggests -y \
Expand All @@ -37,40 +37,40 @@ RUN apt-get install -y \

# Install MIRTK/SVRTK
RUN git clone https://github.com/SVRTK/MIRTK.git \
&& mkdir -p /home/MIRTK/Packages/SVRTK
RUN git clone https://github.com/SVRTK/SVRTK.git /home/MIRTK/Packages/SVRTK \
&& mkdir -p /home/MIRTK/build \
&& cd /home/MIRTK/build \
&& mkdir -p /bin/MIRTK/Packages/SVRTK
RUN git clone https://github.com/SVRTK/SVRTK.git /bin/MIRTK/Packages/SVRTK \
&& mkdir -p /bin/MIRTK/build \
&& cd /bin/MIRTK/build \
&& cmake -D WITH_TBB="ON" -D MODULE_SVRTK="ON" .. \
&& make -j

ENV PATH="$PATH:/home/MIRTK/build/bin:/home/MIRTK/build/lib/tools"
ENV PATH="$PATH:/bin/MIRTK/build/bin:/bin/MIRTK/build/lib/tools"

WORKDIR /var/monai


# Add 3D UNet model weights & execution script
# Add MONAI 3D UNet model weights & execution script

WORKDIR /home

# Setup 3D UNet models
RUN git clone https://github.com/SVRTK/Segmentation_FetalMRI.git --branch svrtk-docker-gpu-0.10 --single-branch /home/Segmentation_FetalMRI
RUN git clone https://github.com/SVRTK/auto-proc-svrtk.git /home/auto-proc-svrtk
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Most of the errors are to do with this line currently. You've changed the location of the recon Shell script, but not updated the rest of the Dockerfile and Python code to reflect the new script location, so... see other comments where I can see you need to make changes.

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i fixed paths and was able to run monai-deploy run ghcr.io/svrtk/aide-svrtk/map:0.2.1 input/ output/


RUN wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/checkpoints-brain-loc-2-labels/latest.ckpt -P /home/Segmentation_FetalMRI/trained-models/checkpoints-brain-loc-labels \
&& wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/checkpoints-brain-loc-2-labels-cropped/latest.ckpt -P /home/Segmentation_FetalMRI/trained-models/checkpoints-brain-loc-labels-cropped \
&& wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/checkpoints-brain-reo-5-labels/latest.ckpt -P /home/Segmentation_FetalMRI/trained-models/checkpoints-brain-reorientation \
&& wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/checkpoints-brain-reo-5-labels-raw-stacks/latest.ckpt -P /home/Segmentation_FetalMRI/trained-models/checkpoints-brain-reorientation-stacks
RUN wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/monai-checkpoints-atunet-brain_bet_all_degree_raw_stacks-1-lab/best_metric_model.pth -P /home/auto-proc-svrtk/trained-models/monai-checkpoints-atunet-brain_bet_all_degree_raw_stacks-1-lab \
&& wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/monai-checkpoints-unet-global-loc-2-lab/best_metric_model.pth -P /home/auto-proc-svrtk/trained-models/monai-checkpoints-unet-global-loc-2-lab \
&& wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/monai-checkpoints-unet-svr-brain-reo-5-lab/best_metric_model.pth -P /home/auto-proc-svrtk/trained-models/monai-checkpoints-unet-svr-brain-reo-5-lab \
&& wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/monai-checkpoints-unet-svr-brain-reo-raw-stacks-5-lab/best_metric_model.pth -P /home/auto-proc-svrtk/trained-models/monai-checkpoints-unet-svr-brain-reo-raw-stacks-5-lab

# Install Python packages
RUN python -m pip install -r /home/Segmentation_FetalMRI/requirements.txt
RUN python -m pip install -r /home/auto-proc-svrtk/config/requirements.txt

# Bugfix: without below, cannot import torch within Python
# Error: OSError: /opt/hpcx/ompi/lib/libmpi.so.40: undefined symbol: opal_hwloc201_hwloc_get_type_depth
# Fix: https://forums.developer.nvidia.com/t/issues-building-docker-image-from-ngc-container-nvcr-io-nvidia-pytorch-22-py3/209034/5
ENV PATH="${PATH}:/opt/hpcx/ompi/bin"
ENV LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/opt/hpcx/ompi/lib"

COPY docker-recon-brain-auto.bash /home/scripts/docker-recon-brain-auto.bash
COPY /home/auto-proc-svrtk/scripts/auto-brain-reconstruction-aide.sh /home/scripts/auto-brain-reconstruction.sh
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You can remove this line entirely. The COPY command in Docker copies from your local machine into the corresponding place in the container. It fails here because /home/auto-proc-svrtk/scripts/auto-brain-reconstruction-aide.sh doesn't exist in the aide-svrtk repo.

Instead, you clone the auto-proc-svrtk repo into the container further up this file, which means auto-brain-reconstruction.sh will be downloaded into the container already.

One thing I noticed – you have two scripts in here, one of which is labelled "aide". Make sure you are pointing at the correct script.

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updated thank you

RUN mkdir -p /home/recon \
&& mkdir -p /home/output \
&& chmod +x /home/scripts/*
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The most important thing here is the chmod on the scripts folder. This enables the Docker container to run the shell scripts in the folder. You need to update this so that it points at the correct folder in the cloned auto-proc-svrtk repo.

I think you can remove the mkdir lines – I don't think they are needed anymore.

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updated thank you

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