TMS_To_MRI_Mapping_Script.ipynb

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     "text": [
      "Collecting xlsxwriter\n",
      "  Downloading XlsxWriter-3.0.2-py3-none-any.whl (149 kB)\n",
      "\u001b[K     |████████████████████████████████| 149 kB 2.2 MB/s eta 0:00:01\n",
      "\u001b[?25hInstalling collected packages: xlsxwriter\n",
      "Successfully installed xlsxwriter-3.0.2\n",
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": [
    "# Last revision 12/1/2021: Ryan Cali "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Note that some of these packages might need to be installed, as they are not on the Martinos server natively...\n",
    "import os\n",
    "import nibabel as nb\n",
    "from glob import glob\n",
    "import numpy as np\n",
    "from os import listdir\n",
    "from os.path import isfile, join\n",
    "import sys\n",
    "import pandas as pd\n",
    "import mne\n",
    "from mne.transforms import apply_trans\n",
    "import openpyxl \n",
    "import re\n",
    "import xlsxwriter\n",
    "import shutil\n",
    "from pathlib import Path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "Specify path to MRI data (Must be isotropic): /autofs/space/nicc_001/data/TMS-EEG/sourcedata/sub-ou1neuroc003/MRI/ou1neuroc003/MEMPRAGE_4e_p2_1mm_iso/007/MPRAGE.nii\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "File path found.\n"
     ]
    }
   ],
   "source": [
    "#-----------MRI portion------------\n",
    "\n",
    "# Specify input path to T1w image as such: /autofs/space/nicc_001/data/TMS-EEG/sourcedata/sub-ou1neuroc003/MRI/ou1neuroc003/MEMPRAGE_4e_p2_1mm_iso/007/MPRAGE.nii \n",
    "\n",
    "user_in = input('Specify path to MRI data (Must be isotropic):')\n",
    "if os.path.exists(user_in):\n",
    "    print('')\n",
    "    print('File path found.')\n",
    "    \n",
    "else:\n",
    "    print('ERROR: File path not found.')\n",
    "    \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "[1. 1. 1.]\n",
      "Isotropic volume found.\n",
      "Image dimensions: [256, 256, 176]\n"
     ]
    }
   ],
   "source": [
    "nii = nb.load(user_in)\n",
    "\n",
    "img = nii.get_fdata()\n",
    "\n",
    "examine_header = nii.header\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "voxel_dims = (nii.header[\"pixdim\"])[1:4]\n",
    "print('')\n",
    "print(voxel_dims)\n",
    "isotropic_target = [1, 1, 1]\n",
    "\n",
    "if (voxel_dims==isotropic_target).all():\n",
    "    \n",
    "    print('Isotropic volume found.')\n",
    "    \n",
    "\n",
    "else:\n",
    "    \n",
    "    print('')\n",
    "    print('ERROR: This program expects an isotropic image (e.g., 1x1x1 dimensions).')\n",
    "    sys.exit()\n",
    "\n",
    "matrix_dims = (nii.header[\"dim\"])[1:4]\n",
    "MRI_x_dims = matrix_dims[0]\n",
    "MRI_y_dims = matrix_dims[1]\n",
    "MRI_z_dims = matrix_dims[2]\n",
    "\n",
    "print(\"Image dimensions:\",[MRI_x_dims, MRI_y_dims, MRI_z_dims])\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdin",
     "output_type": "stream",
     "text": [
      "Specify path to TMS session spreadsheet data: /autofs/space/nicc_001/data/TMS-EEG/sourcedata/sub-ou1neuroc003/ses-01/ou1neuroc003_ses01.xlsx\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "File path found.\n",
      "/autofs/space/nicc_001/data/TMS-EEG/sourcedata/sub-ou1neuroc003/ses-01/ou1neuroc003_ses01.xlsx\n"
     ]
    }
   ],
   "source": [
    "#-----------TMS portion------------\n",
    "\n",
    "# Specify input path to TMS-EEG sessions spreadsheet file as such: /autofs/space/nicc_001/data/TMS-EEG/sourcedata/sub-ou1neuroc003/ses-01/ou1neuroc003_ses01.xlsx \n",
    "session = input('Specify path to TMS session spreadsheet data:')\n",
    "if os.path.exists(session):\n",
    "    print('')\n",
    "    print('File path found.')\n",
    "    \n",
    "else:\n",
    "    print('ERROR: File path not found.')\n",
    "    sys.exit()\n",
    "\n",
    "\n",
    "\n",
    "print(session)\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/autofs/space/nicc_001/users/rcali/Python/Miniconda/lib/python3.8/site-packages/openpyxl/worksheet/_reader.py:312: UserWarning: Data Validation extension is not supported and will be removed\n",
      "  warn(msg)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Success!\n",
      "\n",
      "MRI transforms written to: /autofs/homes/005/rjc73/TMS_MRI_Coordinates.xlsx\n"
     ]
    }
   ],
   "source": [
    "#-----------CONVERSION PORTION FOR TMS-TO-MRI COORDINATES------------\n",
    "# NO DATA IS OVERWRITTEN. ALL SPREADSHEETS AND DATA REMAIN INTACT AND A NEW SPREADSHEET WILL BE GENERATED AFTER RUNNING. THIS WILL CONVERT EACH TMS-EEG SESSION TO MULTIPLE SHEETS\n",
    "# IN ONE .xlsx file\n",
    " \n",
    "pd.set_option('display.float_format', lambda x: '%.5f' % x)\n",
    "x_col = [19]\n",
    "y_col = [20]\n",
    "z_col = [21]\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "target_cols = x_col + y_col + z_col\n",
    "\n",
    "wb = openpyxl.load_workbook(session)\n",
    "\n",
    "pd.set_option('display.max_rows', None, 'display.max_columns', None)\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "writer = pd.ExcelWriter('TMS_MRI_Coordinates.xlsx', engine='xlsxwriter')\n",
    "\n",
    "\n",
    "for sheet in wb.sheetnames:\n",
    "    if re.findall('Session.+', sheet):\n",
    "        df = pd.read_excel(session, sheet, header=None)\n",
    "        \n",
    "        df1 = df[df.columns[target_cols]]\n",
    "        x_targ = df1[df.columns[19]]\n",
    "        y_targ = df1[df.columns[20]]\n",
    "        z_targ = df1[df.columns[21]]\n",
    "        \n",
    "        \n",
    "        df1 = pd.to_numeric(x_targ,\n",
    "                                     errors = 'coerce')\n",
    "        df2 = pd.to_numeric(y_targ,\n",
    "                                     errors = 'coerce')\n",
    "        df3 = pd.to_numeric(z_targ,\n",
    "                                     errors = 'coerce')\n",
    "        \n",
    "        df1 = MRI_x_dims - df1 / 1\n",
    "        df2 = MRI_z_dims - df2 / 1\n",
    "        df3 = MRI_y_dims - df3 / 1\n",
    "        \n",
    "        \n",
    "        \n",
    "        \n",
    "        df['x_val'] = df1\n",
    "        df['y_val'] = df2\n",
    "        df['z_val'] = df3\n",
    "        \n",
    "        \n",
    "        \n",
    "        MRI_coords = [24, 25, 26]\n",
    "        \n",
    "        df_new = df[df.columns[MRI_coords]]\n",
    "        \n",
    "        x = apply_trans(nii.affine, df_new)\n",
    "        \n",
    "        \n",
    "        a = pd.DataFrame(x)\n",
    "        \n",
    "        r = a.round(3)\n",
    "        \n",
    "        r.to_excel(writer, sheet_name=sheet, header=['RAS_x', 'RAS_y', 'RAS_z'])  \n",
    "      \n",
    "    \n",
    "writer.save() # Add something before this line if you wish to have the writer write to a specific directory, otherwise a new .xlsx spreadsheet will be written to your current wd\n",
    "# where you are running the ipynb. \n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "b = os.getcwd()\n",
    "a = os.path.dirname(session)\n",
    "\n",
    "\n",
    "for src_file in Path(b).glob('*TMS_MRI_Coordinates*'):\n",
    "    shutil.copy(src_file, a)\n",
    "    \n",
    "\n",
    "final_dir = os.path.join(a, src_file)    \n",
    "print('Success!')\n",
    "print('')\n",
    "print('MRI transforms written to:', final_dir)\n",
    "        \n"
   ]
  },
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