update notebook

Author: jdkent

run_and_explore.ipynb

@@ -9,7 +9,7 @@
       "source": [
         "# Neurosynth Compose Notebook\n",
         "\n",
-        "After you've built your meta-analysis on [neurosynth compose](compose.neurosynth.org), you can use this notebook to execute and view the meta-analytic results."
+        "After you've built your meta-analysis on [neurosynth compose](https://compose.neurosynth.org), you can use this notebook to execute and view the meta-analytic results."
       ]
     },
     {
@@ -45,21 +45,9 @@
       "execution_count": null,
       "id": "178c5406-2625-4048-af3c-c01bdb5e1b56",
       "metadata": {
-        "colab": {
-          "base_uri": "https://localhost:8080/"
-        },
-        "id": "178c5406-2625-4048-af3c-c01bdb5e1b56",
-        "outputId": "ed849b76-32ee-40a4-8279-b5d9a998da44"
-      },
-      "outputs": [
-        {
-          "name": "stdout",
-          "output_type": "stream",
-          "text": [
-            "Paste the 12 character ID of the meta-analysis here:  6YA5FqTPNJEq\n"
-          ]
-        }
-      ],
+        "id": "178c5406-2625-4048-af3c-c01bdb5e1b56"
+      },
+      "outputs": [],
       "source": [
         "#@title Set your Neurosynth-Compose Meta-Analysis ID { run: \"auto\" }\n",
         "META_ID = input(\"Paste the 12 character ID of the meta-analysis here: \")  # for example: \"8dJ6tG7wfbyS\"\n",
@@ -88,7 +76,7 @@
       },
       "outputs": [],
       "source": [
-        "from nimare.workflows import compose_workflow  #  special workflow to run meta-analysis"
+        "from pynsc.run import run  #  special workflow to run meta-analysis"
       ]
     },
     {
@@ -101,7 +89,7 @@
       "outputs": [],
       "source": [
         "if META_ID is not None:\n",
-        "    meta_result = compose_workflow(META_ID)\n",
+        "    _, meta_result = run(META_ID)\n",
         "else:\n",
         "    print(\"UPDATE META_ID VARIABLE TO YOUR META-ANALYSIS\")"
       ]
@@ -154,7 +142,7 @@
       },
       "outputs": [],
       "source": [
-        "STAT_NAME = \"z\"\n",
+        "STAT_NAME = \"z\" # you will typically only want to look at corrected output\n",
         "stat_map = meta_result.get_map(STAT_NAME)"
       ]
     },
@@ -171,52 +159,56 @@
       ]
     },
     {
-      "cell_type": "markdown",
-      "id": "b43d40b3-9c1d-490c-a3a2-173e04755932",
+      "cell_type": "code",
+      "source": [
+        "# here are your for tables\n",
+        "print(\"\\n\".join(list(meta_result.tables.keys())))"
+      ],
       "metadata": {
-        "id": "b43d40b3-9c1d-490c-a3a2-173e04755932"
+        "id": "sFqMmeQ-xNvM"
       },
-      "source": [
-        "## Investigate what studies contributed to which clusters\n",
-        "\n",
-        "Dive into your results to discover which analyses are driving your results."
-      ]
+      "id": "sFqMmeQ-xNvM",
+      "execution_count": null,
+      "outputs": []
     },
     {
       "cell_type": "code",
-      "execution_count": null,
-      "id": "5732cece-ec55-44cb-996c-e56a26ba1639",
+      "source": [
+        "# get a cluster table\n",
+        "cluster_key = next(t for t in meta_result.tables.keys() if \"clust\" in t)\n",
+        "meta_result.tables[cluster_key]"
+      ],
       "metadata": {
-        "id": "5732cece-ec55-44cb-996c-e56a26ba1639"
+        "id": "qgm3KfxqyD34"
       },
-      "outputs": [],
-      "source": [
-        "from nimare.diagnostics import FocusCounter # Only works for coordinate-based meta-analyses\n",
-        "fc = FocusCounter(target_image=STAT_NAME)"
-      ]
+      "id": "qgm3KfxqyD34",
+      "execution_count": null,
+      "outputs": []
     },
     {
-      "cell_type": "code",
-      "execution_count": null,
-      "id": "2908b852-a2c4-4f8e-92ce-436ab79ce5f9",
+      "cell_type": "markdown",
+      "id": "b43d40b3-9c1d-490c-a3a2-173e04755932",
       "metadata": {
-        "id": "2908b852-a2c4-4f8e-92ce-436ab79ce5f9"
+        "id": "b43d40b3-9c1d-490c-a3a2-173e04755932"
       },
-      "outputs": [],
       "source": [
-        "contribution_table, cluster_img = fc.transform(meta_result)"
+        "## Investigate what studies contributed to which clusters\n",
+        "\n",
+        "Dive into your results to discover which analyses are driving your results."
       ]
     },
     {
       "cell_type": "code",
       "execution_count": null,
-      "id": "eaa9b534-d3ac-4b02-bc90-2aa60fec62c1",
+      "id": "5732cece-ec55-44cb-996c-e56a26ba1639",
       "metadata": {
-        "id": "eaa9b534-d3ac-4b02-bc90-2aa60fec62c1"
+        "id": "5732cece-ec55-44cb-996c-e56a26ba1639"
       },
       "outputs": [],
       "source": [
-        "contribution_table"
+        "# Only works for coordinate-based meta-analyses\n",
+        "diagnostic_key = next(t for t in meta_result.tables.keys() if \"clust\" not in t)\n",
+        "meta_result.tables[diagnostic_key]"
       ]
     }
   ],
@@ -244,4 +236,4 @@
   },
   "nbformat": 4,
   "nbformat_minor": 5
-}
+}