Add SCT and dcm2niix installation instructions

README.md

@@ -2,8 +2,84 @@
 
 Repository containing pipeline for processing spinal cord injury (SCI) patients (both DCM and tSCI) using the [Spinal Cord Toolbox (SCT)](https://github.com/spinalcordtoolbox/spinalcordtoolbox).
 
-Steps:
+Pipeline steps:
 1. DICOM to nii (BIDS) conversion
 2. Processing (spinal cord and lesion segmentation, vertebral labeling)
 3. Quality control (QC) + manual compression level labeling
 4. Lesion metric computation
+
+
+## Dependencies
+
+[Spinal Cord Toolbox v6.4](https://github.com/spinalcordtoolbox/spinalcordtoolbox/releases/tag/6.4)
+[dcm2niix >= v1.0.20220505](https://github.com/rordenlab/dcm2niix?tab=readme-ov-file#install)
+
+## Installation
+
+### SCT Installation
+
+1. Open a new terminal:
+
+Press <kbd>command</kbd> + <kbd>space</kbd> and type `Terminal` and press <kbd>return/enter</kbd>.
+
+2. Run the following commands in the terminal (you can copy-paste the whole block):
+
+> [!NOTE]
+> The installation process will take a few minutes.
+
+```bash
+# Go to your home directory
+cd ~
+# Download SCT v6.4
+wget https://github.com/spinalcordtoolbox/spinalcordtoolbox/archive/refs/tags/6.4.zip
+# Unzip the downloaded file --> the unzipped directory will be named spinalcordtoolbox-6.4
+unzip 6.4.zip
+rm 6.4.zip
+# Go to the SCT directory
+cd spinalcordtoolbox-6.4
+# Install SCT v6.4
+./install_sct -iyc
+#  '-i'   Install in-place (i.e., in the current directory)
+#  '-y'   Install without interruption with 'yes' as default answer
+#  '-c'   Disables sct_check_dependencies so we can check it separately
+```
+
+> [!NOTE]
+> We are not using `git clone` because Apple Developer Tools are needed for `git`.
+
+3. Check that SCT was installed correctly:
+
+Close the terminal and open a new one (press <kbd>command</kbd> + <kbd>space</kbd> and type `Terminal` and press <kbd>return/enter</kbd>.).
+
+```bash
+sct_check_dependencies
+echo $SCT_DIR
+```
+
+The expected output is `[OK]` for all dependencies.
+
+### dcm2niix Installation
+
+1. Open a new terminal (if you closed the previous one):
+
+Press <kbd>command</kbd> + <kbd>space</kbd> and type `Terminal` and press <kbd>return/enter</kbd>.
+
+2. Run the following commands in the terminal (you can copy-paste the whole block):
+
+```bash
+# Go to the SCT directory
+cd $SCT_DIR
+# Activate SCT conda environment
+source ./python/etc/profile.d/conda.sh
+conda activate venv_sct
+# Install dcm2niix using pip
+pip install dcm2niix
+```
+
+3. Check that `dcm2niix` was installed correctly:
+
+```bash
+dcm2niix --version
+```
+
+The expected output is the version of `dcm2niix`.