diff --git a/data_processing.ipynb b/data_processing.ipynb index 5bb6feb..415fcf8 100644 --- a/data_processing.ipynb +++ b/data_processing.ipynb @@ -70,6 +70,40 @@ "Slow processes are indicated with the emoji ⏳" ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "7b784c41", + "metadata": {}, + "outputs": [], + "source": [ + "# Install packages on system\n", + "# ℹ️ No need to run this cell if you run this notebook locally and already have these dependencies installed.\n", + "\n", + "!sudo apt-get update\n", + "!sudo apt-get install git-annex\n", + "\n", + "# Install Python libaries\n", + "!wget -O requirements.txt https://raw.githubusercontent.com/shimming-toolbox/rf-shimming-7t/main/requirements.txt\n", + "!pip install -r requirements.txt" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "90f76ac9", + "metadata": {}, + "outputs": [], + "source": [ + "# Install SCT\n", + "# ℹ️ No need to run this cell if you run this notebook locally and already have SCT installed.\n", + "\n", + "!git clone --depth 1 https://github.com/spinalcordtoolbox/spinalcordtoolbox.git\n", + "!yes | spinalcordtoolbox/install_sct\n", + "# Add SCT's binaries to environment PATH\n", + "os.environ['PATH'] += f\":/content/spinalcordtoolbox/bin\"" + ] + }, { "cell_type": "code", "execution_count": null,