Added deps install for Colab

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,