Merge pull request #8 from UCL-ARC/km/add-new-script

Add dockerfiles and latest analysis script

.gitignore

@@ -0,0 +1,3 @@
+docker_log.txt
+code/
+data/

.pre-commit-config.yaml

@@ -3,6 +3,7 @@ repos:
     rev: v1.5.5
     hooks:
       - id: forbid-tabs
+      - id: remove-tabs
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
@@ -19,7 +20,9 @@ repos:
     hooks:
       - id: hadolint
         args:
+          - --failure-threshold=warning
           - --ignore=DL3008
+          - --ignore=DL3007
   - repo: https://github.com/crate-ci/typos
     rev: v1.24.1
     hooks:
@@ -39,5 +42,7 @@ repos:
     hooks:
       - id: shellcheck
         args:
+          - --severity=warning
           - --external-sources
           - --shell=bash
+          - --exclude=SC2207

Dockerfile

@@ -0,0 +1,29 @@
+FROM cvriend/pgs:latest
+WORKDIR /
+
+# Need fslinstaller.py
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    wget \
+    bc \
+    dc \
+    tree \
+    parallel \
+    zip && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py && python fslinstaller.py -d /usr/local/fsl/ -V 6.0.7.13
+
+RUN echo '\n # FSL Setup \nFSLDIR=/usr/local/fsl \nPATH=${FSLDIR}/share/fsl/bin:${PATH} \nexport FSLDIR PATH \n. ${FSLDIR}/etc/fslconf/fsl.sh' >> /root/.bashrc
+
+COPY analysis_script.sh .
+
+RUN mkdir /data
+RUN mkdir /code
+
+RUN chmod +x analysis_script.sh
+
+CMD ["/analysis_script.sh"]
+
+ENTRYPOINT []

README.md

@@ -1,3 +1,58 @@
 # Enigma-PD-WML
 
-Segment White Mater Lesions (WML) in T1-weighted and FLAIR MR images using FSL and U-Net
+Segment White Mater Lesions (WML) in T1-weighted and FLAIR MRI images using FSL and U-Net
+
+## Build and run the docker container
+
+- Clone this repository
+
+```bash
+git clone https://github.com/UCL-ARC/Enigma-PD-WML.git
+```
+
+- Build the docker image
+
+```bash
+cd Enigma-PD-WML
+docker build -f Dockerfile -t fsl_test .
+```
+
+- Create `code` and `data` directories inside the `Enigma-PD-WML` directory
+
+- Create a `subjects.txt` file at `Enigma-PD-WML/data/subjects.txt`.
+  This file should contain subject identifiers (one per line).
+
+- For each subject id:
+  - Create a directory at `Enigma-PD-WML/data/subject-id` (replacing 'subject-id' with the relevant id from
+    your `subjects.txt` file)
+
+  - Create a sub-directory inside the 'subject-id' directory called `niftis`.
+
+  - Inside `niftis` place the subject's T1 MRI scan and FLAIR MRI scan. Both these files should be in nifti format
+    (ending `.nii.gz`) and contain either `T1` or `FLAIR` in their name respectively.
+
+- Your final file structure should look like below (for two example subject ids):
+
+```bash
+Enigma-PD-WML
+│
+├───code
+│
+└───data
+    ├───subject-1
+    │   └───niftis
+    │       ├───T1.nii.gz
+    │       └───FLAIR.nii.gz
+    │
+    ├───subject-2
+    │   └───niftis
+    │       ├───T1.nii.gz
+    │       └───FLAIR.nii.gz
+    └───subjects.txt
+```
+
+- Run the docker container. Make sure you are in the `Enigma-PD-WML` directory when you run this command.
+
+```bash
+./docker_runscript.sh
+```

_typos.toml

@@ -0,0 +1,3 @@
+[default.extend-words]
+# Don't correct -thr option
+thr = "thr"