add GLM analysis section

Author: aaronjnewman

8-mri/fmri_glm.ipynb

@@ -12,7 +12,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 1,
    "id": "11ebf871",
    "metadata": {},
    "outputs": [],
@@ -51,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "id": "1179daa0",
    "metadata": {},
    "outputs": [
@@ -91,7 +91,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "id": "6546e085",
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    "outputs": [],
@@ -120,7 +120,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "id": "777d7579",
    "metadata": {},
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@@ -156,7 +156,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "id": "340d3f6f",
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@@ -229,7 +229,7 @@
   },
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-   "execution_count": 7,
+   "execution_count": 6,
    "id": "066d0cc0",
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@@ -272,7 +272,7 @@
   },
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-   "execution_count": 8,
+   "execution_count": 7,
    "id": "032c5de0",
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@@ -308,7 +308,7 @@
   },
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+   "execution_count": 8,
    "id": "59f716e8",
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@@ -350,7 +350,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "id": "20df407e",
    "metadata": {},
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@@ -403,7 +403,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "id": "995e8fa4",
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@@ -458,7 +458,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "id": "e106e87b",
    "metadata": {},
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@@ -513,7 +513,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "id": "aa7b9dc1",
    "metadata": {},
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@@ -620,7 +620,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 13,
    "id": "2630ea0c",
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@@ -737,7 +737,7 @@
   },
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-   "execution_count": 15,
+   "execution_count": 14,
    "id": "7bbe06c1",
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@@ -793,7 +793,7 @@
   },
   {
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-   "execution_count": 16,
+   "execution_count": 15,
    "id": "cec2a080",
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@@ -839,7 +839,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 16,
    "id": "9aaf4a75",
    "metadata": {},
    "outputs": [
@@ -859,6 +859,55 @@
     "plot_design_matrix(design_matrix)  \n",
     "plt.show()"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "49719602",
+   "metadata": {},
+   "source": [
+    "## Run the GLM Analysis"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "8f03a7c0",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/nq/chbqhzjx5hb6hfjx708rh2_40000gn/T/ipykernel_15985/2329769883.py:4: UserWarning: If design matrices are supplied, [t_r] will be ignored.\n",
+      "  first_level_model = first_level_model.fit(bold_img, design_matrices=design_matrix)\n"
+     ]
+    }
+   ],
+   "source": [
+    "# run the GLM analysis\n",
+    "from nilearn.glm.first_level import FirstLevelModel\n",
+    "first_level_model = FirstLevelModel(t_r=tr_sec, hrf_model='glover', high_pass=0.01)\n",
+    "first_level_model = first_level_model.fit(bold_img, design_matrices=design_matrix)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "602630d3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Define contrasts\n",
+    "contrast_motion = np.array([1 if 'motion' in name else 0 for name in design_matrix.columns])\n",
+    "# Estimate contrast\n",
+    "z_map_motion = first_level_model.compute_contrast(contrast_motion, output_type='z_score')\n",
+    "# Plot the resulting z-map\n",
+    "plt.rcParams['figure.figsize'] = [12.5, 10]\n",
+    "from nilearn.plotting import plot_stat_map\n",
+    "plot_stat_map(z_map_motion, bg_img=anat_img, threshold=3.0,\n",
+    "              title='Z-map for Motion Contrast (thresholded at z>3.0)')\n",
+    "show()      "
+   ]
   }
  ],
  "metadata": {