upated notebook added

notebooks/BraTS_2023_running_instructions.ipynb

@@ -0,0 +1,185 @@
+{
+  "nbformat": 4,
+  "nbformat_minor": 0,
+  "metadata": {
+    "colab": {
+      "provenance": []
+    },
+    "kernelspec": {
+      "name": "python3",
+      "display_name": "Python 3"
+    },
+    "language_info": {
+      "name": "python"
+    }
+  },
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": 1,
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "id": "cRch6DI49jre",
+        "outputId": "f7cceeee-d868-44e0-932b-b58b0cc5f8ec"
+      },
+      "outputs": [
+        {
+          "output_type": "stream",
+          "name": "stdout",
+          "text": [
+            "Mounted at /gdrive\n"
+          ]
+        }
+      ],
+      "source": [
+        "# mount google drive\n",
+        "from google.colab import drive\n",
+        "drive.mount('/gdrive')"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# Set up your working directory in google drive, so you dont loss the progress\n",
+        "root_dir = \"/gdrive/MyDrive\"\n",
+        "\n",
+        "\n",
+        "# create a directory in MyDrive\n",
+        "directory_name = \"BraTS_segmentation\"\n",
+        "import os\n",
+        "\n",
+        "working_dir = os.path.join(root_dir, directory_name)\n",
+        "os.makedirs(working_dir, exist_ok=True)\n",
+        "os.chdir(working_dir)"
+      ],
+      "metadata": {
+        "id": "wS0HgrhK96FL"
+      },
+      "execution_count": 4,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "%pwd"
+      ],
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/",
+          "height": 35
+        },
+        "id": "Ny8P_EUq-igv",
+        "outputId": "b020cb63-7ee9-4f95-8225-0ad7bcc55bea"
+      },
+      "execution_count": 4,
+      "outputs": [
+        {
+          "output_type": "execute_result",
+          "data": {
+            "text/plain": [
+              "'/gdrive/MyDrive/BraTS_segmentation'"
+            ],
+            "application/vnd.google.colaboratory.intrinsic+json": {
+              "type": "string"
+            }
+          },
+          "metadata": {},
+          "execution_count": 4
+        }
+      ]
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# clone the repo from Github\n",
+        "!git clone https://github.com/faizan1234567/BraTS23-Tumors-Segmentation\n",
+        "%cd BraTS23-Tumors-Segmentation\n"
+      ],
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "id": "xrBqNqFQ9xdA",
+        "outputId": "c7a0b1ee-3e78-4648-c18e-a5e5e41f46c9"
+      },
+      "execution_count": 5,
+      "outputs": [
+        {
+          "output_type": "stream",
+          "name": "stdout",
+          "text": [
+            "Cloning into 'BraTS23-Tumors-Segmentation'...\n",
+            "remote: Enumerating objects: 1553, done.\u001b[K\n",
+            "remote: Counting objects: 100% (285/285), done.\u001b[K\n",
+            "remote: Compressing objects: 100% (174/174), done.\u001b[K\n",
+            "remote: Total 1553 (delta 149), reused 219 (delta 93), pack-reused 1268 (from 1)\u001b[K\n",
+            "Receiving objects: 100% (1553/1553), 32.51 MiB | 16.40 MiB/s, done.\n",
+            "Resolving deltas: 100% (858/858), done.\n",
+            "/gdrive/MyDrive/BraTS_segmentation/BraTS23-Tumors-Segmentation\n"
+          ]
+        }
+      ]
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# now install all the required dependencies\n",
+        "!pip install -r requirements.txt\n",
+        "# virtual enviroment recommended"
+      ],
+      "metadata": {
+        "id": "mCTSqI-P-qJI"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "markdown",
+      "source": [
+        "# Restart Runtime"
+      ],
+      "metadata": {
+        "id": "jukUO1gG_s0M"
+      }
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "# run the working directory cell to navigate to working directory"
+      ],
+      "metadata": {
+        "id": "r56xxBZQAaz3"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "%pwd"
+      ],
+      "metadata": {
+        "id": "gy8Nw5vDAhqW"
+      },
+      "execution_count": null,
+      "outputs": []
+    },
+    {
+      "cell_type": "code",
+      "source": [
+        "!python train.py -h\n",
+        "\n",
+        "# setup your data path and other params in the configs direcdtory\n",
+        "# then run python trian.py\n",
+        "# python test.py"
+      ],
+      "metadata": {
+        "id": "KGsLUzXY_0NL"
+      },
+      "execution_count": null,
+      "outputs": []
+    }
+  ]
+}