Cortical AD signature.ipynb

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   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>side</th>\n",
       "      <th>measurement</th>\n",
       "      <th>region</th>\n",
       "      <th>value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>right</td>\n",
       "      <td>SurfArea</td>\n",
       "      <td>bankssts</td>\n",
       "      <td>969</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>right</td>\n",
       "      <td>SurfArea</td>\n",
       "      <td>caudalanteriorcingulate</td>\n",
       "      <td>679</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>right</td>\n",
       "      <td>SurfArea</td>\n",
       "      <td>caudalmiddlefrontal</td>\n",
       "      <td>2092</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>right</td>\n",
       "      <td>SurfArea</td>\n",
       "      <td>cuneus</td>\n",
       "      <td>1788</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>right</td>\n",
       "      <td>SurfArea</td>\n",
       "      <td>entorhinal</td>\n",
       "      <td>450</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "     side measurement                   region value\n",
       "44  right    SurfArea                 bankssts   969\n",
       "45  right    SurfArea  caudalanteriorcingulate   679\n",
       "46  right    SurfArea      caudalmiddlefrontal  2092\n",
       "47  right    SurfArea                   cuneus  1788\n",
       "48  right    SurfArea               entorhinal   450"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Let's first fetch some FreeSurfer results\n",
    "import pyxnat\n",
    "x = pyxnat.Interface(config='/home/grg/.xnat_bsc.cfg')\n",
    "exp = x.select.experiment('BBRC_E00080')\n",
    "res = exp.resource('FREESURFER6_HIRES')\n",
    "aparc = res.aparc()\n",
    "\n",
    "# DataFrame should look like this\n",
    "aparc.query('measurement == \"SurfArea\"').head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2.338209274795409"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "regions = ['entorhinal', 'inferiortemporal', 'middletemporal', 'fusiform']\n",
    "# ROIs from Jack et al., Alzheimers Dement. 2017; doi:10.1016/j.jalz.2016.08.005\n",
    "\n",
    "weighted_sum = 0\n",
    "total_surf_area = 0\n",
    "\n",
    "# For each region/hemisphere\n",
    "for r in regions:\n",
    "    for s in ['left', 'right']:\n",
    "        \n",
    "        # Filter the DataFrame using current region/hemisphere\n",
    "        roi = aparc.query('region == \"%s\" & side == \"%s\"'%(r, s))\n",
    "        \n",
    "        # Get cortical thickness\n",
    "        thickness = float(roi.query('measurement == \"ThickAvg\"').value)\n",
    "        \n",
    "        # Get surface area\n",
    "        surf_area = float(roi.query('measurement == \"SurfArea\"').value)\n",
    "        \n",
    "        # Add them to the total sum\n",
    "        weighted_sum += thickness * surf_area\n",
    "        total_surf_area += surf_area\n",
    "        \n",
    "# The final result is the ratio between both values\n",
    "final = weighted_sum / total_surf_area\n",
    "final"
   ]
  }
 ],
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