update the notebook to include more documentation

Author: jdkent

run_and_explore.ipynb

@@ -1,13 +1,27 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "69c306a1-f24a-410a-b034-f002bc0b7a97",
+   "metadata": {},
+   "source": [
+    "# Neurosynth Compose Notebook\n",
+    "\n",
+    "After you've built your meta-analysis on neurosynth compose, you can use this notebook to execute and view the meta-analytic results.\n",
+    "All you need is to "
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "28d0e8b6-9bbd-4256-a19a-ff36eeca5cfd",
    "metadata": {},
    "outputs": [],
    "source": [
+    "#@title 1) Run once to install NiMARE (~1 minute)\n",
+    "%%capture --no-display --no-stderr\n",
     "%%bash\n",
+    "wget https://raw.githubusercontent.com/neurostuff/neurosynth-compose-notebook/main/requirements.txt\n",
     "pip install -r requirements.txt"
    ]
   },
@@ -16,7 +30,9 @@
    "id": "37860b1b-5031-4bd7-8e86-c668f545126b",
    "metadata": {},
    "source": [
-    "## INSERT YOUR META-ANALYSIS ID HERE"
+    "## INSERT YOUR META-ANALYSIS ID HERE\n",
+    "\n",
+    "This is the id for your specific meta-analysis"
    ]
   },
   {
@@ -26,7 +42,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "META_ID = \"3SD2A7LGuQTm\""
+    "#@title 2) Set your Neurosynth-Compose Meta-Analysis ID { run: \"auto\" }\n",
+    "\n",
+    "META_ID = None  # for example: \"8dJ6tG7wfbyS\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7dccf070-a1cc-4471-97f1-d386374a80df",
+   "metadata": {},
+   "source": [
+    "## Run your selected Meta-Analysis\n",
+    "\n",
+    "A workflow in NiMARE will interpret the meta-analysis you specified and\n",
+    "run the selected algorithm and corrector (optional) on the studyset selected."
    ]
   },
   {
@@ -36,8 +65,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from nimare.workflows import compose_run\n",
-    "from nilearn.plotting import plot_stat_map"
+    "from nimare.workflows import compose_run  #  special workflow to run meta-analysis"
    ]
   },
   {
@@ -61,7 +89,19 @@
    },
    "source": [
     "## Choose which statistical map to investigate\n",
-    "default is z map, but each estimator/corrector combination may generate corrected/more appropriate statistical maps for summary/investigation"
+    "\n",
+    "The Default is the z map, but each estimator/corrector combination may generate\n",
+    "corrected/more appropriate statistical maps for investigation."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "347e806d-a264-416e-8d52-8f9574bd3a58",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from nilearn.plotting import plot_stat_map  # display statistical images"
    ]
   },
   {
@@ -101,7 +141,9 @@
    "id": "b43d40b3-9c1d-490c-a3a2-173e04755932",
    "metadata": {},
    "source": [
-    "## Investigate what studies contributed to which clusters"
+    "## Investigate what studies contributed to which clusters\n",
+    "\n",
+    "Dive into your results to discover which analyses are driving your results."
    ]
   },
   {