14 monai thorax 3d pipeline

README.md

@@ -3,7 +3,7 @@
 <p align="center">
 <h1 align="center">aide-svrtk</h1>
 <p align="center">
-  AI-driven, automated <a href="https://github.com/SVRTK/SVRTK">SVR reconstruction</a> packaged as an AIDE Application, based on 
+  AI-driven, <a href="https://github.com/SVRTK/auto-proc-svrtk">automated</a> version of <a href="https://github.com/SVRTK/SVRTK">SVR reconstruction</a> packaged as an AIDE Application, based on 
   the open-source <a href="https://github.com/Project-MONAI/monai-deploy/blob/main/guidelines/monai-application-package.md">
   MONAI Application Package (MAP)</a> standard.
   <br />
@@ -20,14 +20,14 @@
 
 The slice-to-volume reconstruction toolkit ([SVRTK](https://github.com/SVRTK/SVRTK)) is an image-based registration 
 framework for reconstruction of 3D volumes from multiple 2D image slices. SVRTK is used extensively for performing 
-motion-corrected reconstruction of MRI data. 
+motion-corrected reconstruction of MRI data. The [automated SVR](https://github.com/SVRTK/auto-proc-svrtk) version employs deep learning [MONAI](https://github.com/Project-MONAI/MONAI) networks for localisation and reorientation of the thorax to the standard radiological space.
 
-Currently, this MAP implements SVRTK for reconstruction of 2D **fetal brain MRI** data into motion-corrected 3D volumes. 
+Currently, this MAP implements SVRTK for reconstruction of 2D **fetal thorax MRI** data into motion-corrected 3D volumes. 
 Further MAPs for reconstruction of other fetal organs are in development and coming soon.
 
 [AIDE](https://www.aicentre.co.uk/platforms#view1) is an open-source platform for the deployment of AI applications in 
-healthcare settings. This repo, created and led by [Tom Roberts](https://github.com/tomaroberts), packages automated 
-3D fetal brain MRI reconstruction into a [MONAI Application Package (MAP)](https://github.com/Project-MONAI/monai-deploy) 
+healthcare settings. This repo, created and led by [Tom Roberts](https://github.com/tomaroberts), packages [automated 
+3D fetal thorax MRI reconstruction](https://github.com/SVRTK/auto-proc-svrtk) into a [MONAI Application Package (MAP)](https://github.com/Project-MONAI/monai-deploy) 
 for execution on AIDE, and other platforms compatible with the MAP standard.
 
 ## aide-svrtk MAP workflow
@@ -38,10 +38,10 @@ MRI DICOM Series contained the motion-corrected reconstruction.
 The aide-svrtk MAP consists of three operators:
 1. `dcm2nii_operator.py` – converts the input 2D MRI DICOM Series into NIfTI format required by SVRTK, using 
 [dcm2niix](https://github.com/rordenlab/dcm2niix)
-2. `fetal_mri_3d_brain_recon_operator.py` – runs automated fetal brain SVRTK reconstruction, in three main steps:
-   a. AI-driven brain masking 
-   b. Slice-to-volume registration reconstruction
-   c. AI-driven brain reorientation
+2. `fetal_mri_3d_thorax_recon_operator.py` – runs [automated fetal thorax SVRTK reconstruction](https://github.com/SVRTK/auto-proc-svrtk), in three main steps:
+   a. AI-driven thorax masking 
+   b. Deformable slice-to-volume registration reconstruction
+   c. AI-driven thorax reorientation
 3. `nii2dcm_operator.py` – converts the SVRTK output NIfTI into a 3D DICOM Series, using 
 [nii2dcm](https://github.com/tomaroberts/nii2dcm)
 
@@ -56,7 +56,7 @@ The aide-svrtk MAP consists of three operators:
 
 1. Download
 ```shell
-git clone https://github.com/SVRTK/aide-svrtk.git
+git clone -b 14-monai-thorax-3d-pipeline https://github.com/SVRTK/aide-svrtk.git
 ```
 
 2. Setup virtual env
@@ -98,37 +98,37 @@ The final MAP is called `map`
 
 ```shell
 # Initial packaging of MAP
-monai-deploy package app -t ghcr.io/svrtk/aide-svrtk/map-init:0.2.0 -r requirements.txt -l DEBUG
+monai-deploy package app -t ghcr.io/svrtk/aide-svrtk/map-init:0.2.2 -r requirements.txt -l DEBUG
 
 # Build 3rd-party software on top of MAP
-docker build -t ghcr.io/svrtk/aide-svrtk/map:0.2.0 app/
+docker build -t ghcr.io/svrtk/aide-svrtk/map:0.2.2 app/
 
 # Test MAP with MONAI Deploy
-monai-deploy run ghcr.io/svrtk/aide-svrtk/map:0.2.0 input/ output/
+monai-deploy run ghcr.io/svrtk/aide-svrtk/map:0.2.2 input/ output/
 
 # Push initial MAP and final MAP to GHCR
-docker push ghcr.io/svrtk/aide-svrtk/map-init:0.2.0
-docker push ghcr.io/svrtk/aide-svrtk/map:0.2.0
+docker push ghcr.io/svrtk/aide-svrtk/map-init:0.2.2
+docker push ghcr.io/svrtk/aide-svrtk/map:0.2.2
 ```
 
 ## Optional
 
 Enter Docker container for testing
 
 ```shell
-docker run --gpus all -it --rm -v local/path/to/aide-svrtk/input:/var/monai/input/ --entrypoint /bin/bash ghcr.io/svrtk/aide-svrtk/map:0.2.0
+docker run --gpus all -it --rm -v local/path/to/aide-svrtk/input:/var/monai/input/ --entrypoint /bin/bash ghcr.io/svrtk/aide-svrtk/map:0.2.2
 ```
 
 Run on specified GPU if machine has >1 available
 
 ```shell
-CUDA_VISIBLE_DEVICES=2 monai-deploy run ghcr.io/svrtk/aide-svrtk/map:0.2.0 input/ output/
+CUDA_VISIBLE_DEVICES=2 monai-deploy run ghcr.io/svrtk/aide-svrtk/map:0.2.2 input/ output/
 ```
 
 ## Running on AIDE
 To run aide-svrtk MAP on AIDE, two files from the `app/workflows` directory are required, namely:
-- `fetal-3d-brain-mri.json` – AIDE Clinical Workflow file.
+- `fetal-3d-thorax-mri.json` – AIDE Clinical Workflow file.
   - Effectively a sequence of tasks run on AIDE
-- `fetal-brain-3d-recon-argo-template.yaml` – Argo Workflow Template file.
+- `fetal-thorax-3d-recon-argo-template.yaml` – Argo Workflow Template file.
   - Called by the AIDE Clinical Workflow file. Executes the aide-svrtk MAP using Argo. This is the central task within 
   the AIDE Clinical Workflow file.

app/Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/svrtk/aide-svrtk/map-init:0.2.0 AS build
+FROM ghcr.io/svrtk/aide-svrtk/map-init:0.2.2 AS build
 
 # Add dcm2niix to MAP
 WORKDIR /bin
@@ -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 \
@@ -37,42 +37,52 @@ 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
+
+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 \
+    && wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/monai-checkpoints-unet-stack-body-reo-4-lab/best_metric_model.pth -P /home/auto-proc-svrtk/trained_models/monai-checkpoints-unet-stack-body-reo-4-lab \
+    && wget https://gin.g-node.org/SVRTK/fetal_mri_network_weights/raw/master/monai-checkpoints-unet-thorax-reo-4-lab-cmr/best_metric_model.pth -P /home/auto-proc-svrtk/trained_models/monai-checkpoints-unet-thorax-reo-4-lab-cmr 
+
+
+
 
-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
 
 # 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
-RUN mkdir -p /home/recon \
-    && mkdir -p /home/output \
-    && chmod +x /home/scripts/*
+#COPY /home/auto-proc-svrtk/scripts/auto-thorax-reconstruction-aide.sh /home/scripts/auto-thorax-reconstruction.sh
+
+
+RUN mkdir -p /home/recon 
+RUN mkdir -p /home/output
+RUN mkdir -p /home/scripts
+RUN chmod +x /home/auto-proc-svrtk/scripts/*
+
 
 WORKDIR /var/monai

app/__main__.py

@@ -1,4 +1,4 @@
-from app import FetalMri3dBrainApp
+from app import FetalMri3dThoraxApp
 
 if __name__ == "__main__":
-    FetalMri3dBrainApp(do_run=True)
+    FetalMri3dThoraxApp(do_run=True)

app/app.py

@@ -1,4 +1,4 @@
-# AI-driven 3D fetal brain MRI reconstruction using SVRTK constructed as a MONAI Application Package (MAP)
+# AI-driven 3D fetal thorax MRI reconstruction using SVRTK constructed as a MONAI Application Package (MAP)
 #
 # Tom Roberts (tom.roberts@gstt.nhs.uk / t.roberts@kcl.ac.uk)
 #
@@ -10,18 +10,18 @@
 from monai.deploy.operators.dicom_series_selector_operator import DICOMSeriesSelectorOperator
 
 from operators.dcm2nii_operator import Dcm2NiiOperator
-from operators.fetal_mri_3d_brain_recon_operator import FetalMri3dBrainOperator
+from operators.fetal_mri_3d_thorax_recon_operator import FetalMri3dThoraxOperator
 from operators.nii2dcm_operator import NiftiToDicomWriterOperator
 
 
 @resource(cpu=16, gpu=1, memory="32Gi")
-class FetalMri3dBrainApp(Application):
+class FetalMri3dThoraxApp(Application):
     """
-    Motion-corrected 3D fetal brain MRI Application class
+    Motion-corrected 3D fetal thorax MRI Application class
     """
 
-    name = "3d-fetal-brain-mri"
-    description = "Motion-corrected 3D fetal brain MRI application."
+    name = "3d-fetal-thorax-mri"
+    description = "Motion-corrected 3D fetal thorax MRI application."
     version = "0.2.0"
 
     def compose(self):
@@ -36,8 +36,8 @@ def compose(self):
         # DICOM to NIfTI operator
         dcm2nii_op = Dcm2NiiOperator()
 
-        # Fetal Brain 3D MRI reconstruction operator
-        fetal_mri_3d_recon_op = FetalMri3dBrainOperator()
+        # Fetal Thorax 3D MRI reconstruction operator
+        fetal_mri_3d_recon_op = FetalMri3dThoraxOperator()
 
         # DICOM Writer operator
         nii2dcm_op = NiftiToDicomWriterOperator()
@@ -68,4 +68,4 @@ def compose(self):
 """
 
 if __name__ == "__main__":
-    FetalMri3dBrainApp(do_run=True)
+    FetalMri3dThoraxApp(do_run=True)