Merge branch 'main' into sb/fix-func

.github/workflows/ci.yml

@@ -23,12 +23,12 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Install Python 3
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8.17
+          python-version: 3.8.18
 
       - name: Install dependencies
         run: |

README.md

@@ -31,19 +31,34 @@ Currently supported labels are:
 
 ## 2. Installation
 
+Download the repository:
+
 ```console
 git clone https://github.com/spinalcordtoolbox/manual-correction.git
 cd manual-correction
+```
+
+Create a virtual environment and install the required packages:
+
+```console
 python3 -m venv venv
 source venv/bin/activate
 pip install -r requirements.txt
 ```
 
+Alternatively, you can use existing SCT's conda environment:
+
+```console
+source ${SCT_DIR}/python/etc/profile.d/conda.sh
+conda activate venv_sct
+```
+
 ## 3. Usage
 
 > **Important**
 > All scripts currently assume BIDS-compliant data. For more information about the BIDS standard, please visit http://bids.neuroimaging.io.
 
+---
 
 ### `manual_correction.py`
 
@@ -58,6 +73,8 @@ python manual_correction.py -path-img <INPUT_PATH> -config <CONFIG_FILE>
 
 For full help, please run: `python manual_correction.py -h`.
 
+---
+
 ### `package_for_correction.py`
 
 If the manual correction is done by someone else than the person doing the processing, this script packages the processed images and existing labels (segmentation, disc labels, etc.) and creates a single ZIP file that can conveniently be sent to collaborators.
@@ -71,6 +88,8 @@ python package_for_correction.py -path-in <INPUT_PATH> -config <CONFIG_FILE>
 
 For full help, please run: `python package_for_correction.py -h`.
 
+---
+
 ### `copy_files_to_derivatives.py`
 
 This script copies manually corrected labels (segmentations, disc labels, etc.) from your local `derivatives/labels` folder to the already existing dataset's `derivatives/labels` folder.