SCCORProcessing.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import string\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "import pydicom"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "path = '/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "patients = os.listdir(path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "754"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(patients)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "root_lst = []\n",
    "series_lst = []\n",
    "sid_lst = []\n",
    "pid_lst = []\n",
    "files_lst = []\n",
    "meta_lst = []\n",
    "patient_age_lst = []\n",
    "patient_sex_lst = []\n",
    "scan_modality_lst = []\n",
    "scan_date_lst = []\n",
    "scan_time_lst = []\n",
    "scan_option_lst = []\n",
    "scan_slicethickness_lst = []\n",
    "scan_spacing_lst = []\n",
    "scan_pixel_spacing_1_lst = []\n",
    "scan_pixel_spacing_2_lst = []\n",
    "scan_rows_lst = []\n",
    "scan_cols_lst = []\n",
    "scan_kvp_lst = []\n",
    "scan_xraycurrent_lst = []\n",
    "scan_exposuretime_lst = []\n",
    "\n",
    "i = 0\n",
    "for root, dirs, files in os.walk(path, topdown=True):\n",
    "    if root.count('/') == 10: # if it is a dicom series folder\n",
    "        # use path as the key\n",
    "        root_lst.append(root)\n",
    "        # extract patient id from the path\n",
    "        sub_path = root.split('/')[8]\n",
    "        pid_lst.append(sub_path)\n",
    "        # extract series folder name\n",
    "        series_lst.append(root.split('/')[-1])\n",
    "        # count number of dicom images\n",
    "        files_lst.append(len(files))\n",
    "        # read the first dicom file in current path    \n",
    "        try:\n",
    "            dicom_file_path = os.path.join(root, files[0])\n",
    "            # meta elements in the dicom file\n",
    "            ds = pydicom.filereader.dcmread(dicom_file_path)\n",
    "        except:\n",
    "            ds = None\n",
    "\n",
    "        try:\n",
    "            patient_age_lst.append(ds.PatientAge) # age\n",
    "        except:\n",
    "            patient_age_lst.append(None)\n",
    "        try:\n",
    "            patient_sex_lst.append(ds.PatientSex) # sex\n",
    "        except:\n",
    "            patient_sex_lst.append(None)\n",
    "        try:\n",
    "            scan_modality_lst.append(ds.Modality) # scan modality\n",
    "        except:\n",
    "            scan_modality_lst.append(None)\n",
    "        try:\n",
    "            scan_date_lst.append(ds.AcquisitionDate) # scan date\n",
    "        except:\n",
    "            scan_date_lst.append(None)\n",
    "        try:\n",
    "            scan_time_lst.append(ds.AcquisitionTime) # scan time\n",
    "        except:\n",
    "            scan_time_lst.append(None)\n",
    "        try:\n",
    "            scan_slicethickness_lst.append(ds.SliceThickness) # slice thickness\n",
    "        except:\n",
    "            scan_slicethickness_lst.append(None)\n",
    "        try:\n",
    "            scan_spacing_lst.append(ds.SpacingBetweenSlices) # slice spacing\n",
    "        except:\n",
    "            scan_spacing_lst.append(None)\n",
    "        try:\n",
    "            scan_pixel_spacing_1_lst.append(ds.PixelSpacing[0]) # pixel spacing direction 1\n",
    "        except:\n",
    "            scan_pixel_spacing_1_lst.append(None)\n",
    "        try:\n",
    "            scan_pixel_spacing_2_lst.append(ds.PixelSpacing[1]) # pixel spacing direction 2\n",
    "        except:\n",
    "            scan_pixel_spacing_2_lst.append(None)\n",
    "        try:\n",
    "            scan_rows_lst.append(ds.Rows) # number of pixels per row\n",
    "        except:\n",
    "            scan_rows_lst.append(None)\n",
    "        try:\n",
    "            scan_cols_lst.append(ds.Columns) # number of pixels per column\n",
    "        except:\n",
    "            scan_cols_lst.append(None)\n",
    "        try:\n",
    "            scan_kvp_lst.append(ds.KVP) # kilovoltage applied to the x-ray tube\n",
    "        except:\n",
    "            scan_kvp_lst.append(None)\n",
    "        try:\n",
    "            scan_xraycurrent_lst.append(ds.XRayTubeCurrent) # x-ray current\n",
    "        except:\n",
    "            scan_xraycurrent_lst.append(None)\n",
    "        try:\n",
    "            scan_exposuretime_lst.append(ds.ExposureTime) # exposure time\n",
    "        except:\n",
    "            scan_exposuretime_lst.append(None)\n",
    "    \n",
    "        i += 1\n",
    "    \n",
    "    #if i > 5000:\n",
    "        #break\n",
    "        \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "dicom_profile = {'path':root_lst,\n",
    "                'pid':pid_lst,\n",
    "                'series':series_lst,\n",
    "                'files':files_lst,\n",
    "                'age':patient_age_lst,\n",
    "                'sex':patient_sex_lst,\n",
    "                'modality':scan_modality_lst,\n",
    "                'date': scan_date_lst,\n",
    "                'time': scan_time_lst,\n",
    "                'slice_thickness': scan_slicethickness_lst,\n",
    "                'slice_spacing': scan_spacing_lst,\n",
    "                'pixcel_spacing_1': scan_pixel_spacing_1_lst,\n",
    "                'pixcel_spacing_2': scan_pixel_spacing_2_lst,\n",
    "                'rows':scan_rows_lst,\n",
    "                'columns':scan_cols_lst,\n",
    "                'kvp': scan_kvp_lst,\n",
    "                'x_ray_current': scan_xraycurrent_lst,\n",
    "                'exposure_time': scan_exposuretime_lst\n",
    "                }"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "dicom_profile_df = pd.DataFrame.from_dict(dicom_profile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "        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>age</th>\n",
       "      <th>columns</th>\n",
       "      <th>date</th>\n",
       "      <th>exposure_time</th>\n",
       "      <th>files</th>\n",
       "      <th>kvp</th>\n",
       "      <th>modality</th>\n",
       "      <th>path</th>\n",
       "      <th>pid</th>\n",
       "      <th>pixcel_spacing_1</th>\n",
       "      <th>pixcel_spacing_2</th>\n",
       "      <th>rows</th>\n",
       "      <th>series</th>\n",
       "      <th>sex</th>\n",
       "      <th>slice_spacing</th>\n",
       "      <th>slice_thickness</th>\n",
       "      <th>time</th>\n",
       "      <th>x_ray_current</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>057Y</td>\n",
       "      <td>888.0</td>\n",
       "      <td>20080101</td>\n",
       "      <td>4070.0</td>\n",
       "      <td>1</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.545455</td>\n",
       "      <td>0.596847</td>\n",
       "      <td>733.0</td>\n",
       "      <td>001</td>\n",
       "      <td>M</td>\n",
       "      <td>NaN</td>\n",
       "      <td>400.000000</td>\n",
       "      <td>081707</td>\n",
       "      <td>80.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>057Y</td>\n",
       "      <td>512.0</td>\n",
       "      <td>20080101</td>\n",
       "      <td>400.0</td>\n",
       "      <td>131</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.683594</td>\n",
       "      <td>0.683594</td>\n",
       "      <td>512.0</td>\n",
       "      <td>002</td>\n",
       "      <td>M</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.500000</td>\n",
       "      <td>081818</td>\n",
       "      <td>250.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>057Y</td>\n",
       "      <td>512.0</td>\n",
       "      <td>20080101</td>\n",
       "      <td>400.0</td>\n",
       "      <td>521</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.683594</td>\n",
       "      <td>0.683594</td>\n",
       "      <td>512.0</td>\n",
       "      <td>004</td>\n",
       "      <td>M</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.625000</td>\n",
       "      <td>081818</td>\n",
       "      <td>250.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>057Y</td>\n",
       "      <td>512.0</td>\n",
       "      <td>20080101</td>\n",
       "      <td>400.0</td>\n",
       "      <td>131</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.683594</td>\n",
       "      <td>0.683594</td>\n",
       "      <td>512.0</td>\n",
       "      <td>003</td>\n",
       "      <td>M</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.500000</td>\n",
       "      <td>081818</td>\n",
       "      <td>250.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>064Y</td>\n",
       "      <td>888.0</td>\n",
       "      <td>20140101</td>\n",
       "      <td>4075.0</td>\n",
       "      <td>1</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.545455</td>\n",
       "      <td>0.596847</td>\n",
       "      <td>734.0</td>\n",
       "      <td>001</td>\n",
       "      <td>M</td>\n",
       "      <td>10.000</td>\n",
       "      <td>400.545454</td>\n",
       "      <td>120659.366914</td>\n",
       "      <td>80.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>064Y</td>\n",
       "      <td>512.0</td>\n",
       "      <td>20140101</td>\n",
       "      <td>400.0</td>\n",
       "      <td>542</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.703125</td>\n",
       "      <td>0.703125</td>\n",
       "      <td>512.0</td>\n",
       "      <td>002</td>\n",
       "      <td>M</td>\n",
       "      <td>0.625</td>\n",
       "      <td>0.625000</td>\n",
       "      <td>120749.620649</td>\n",
       "      <td>250.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>064Y</td>\n",
       "      <td>512.0</td>\n",
       "      <td>20140101</td>\n",
       "      <td>400.0</td>\n",
       "      <td>136</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.703125</td>\n",
       "      <td>0.703125</td>\n",
       "      <td>512.0</td>\n",
       "      <td>004</td>\n",
       "      <td>M</td>\n",
       "      <td>0.625</td>\n",
       "      <td>2.500000</td>\n",
       "      <td>120749.620649</td>\n",
       "      <td>250.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>064Y</td>\n",
       "      <td>512.0</td>\n",
       "      <td>20140101</td>\n",
       "      <td>400.0</td>\n",
       "      <td>136</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.703125</td>\n",
       "      <td>0.703125</td>\n",
       "      <td>512.0</td>\n",
       "      <td>003</td>\n",
       "      <td>M</td>\n",
       "      <td>0.625</td>\n",
       "      <td>2.500000</td>\n",
       "      <td>120749.620649</td>\n",
       "      <td>250.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>060Y</td>\n",
       "      <td>512.0</td>\n",
       "      <td>20100101</td>\n",
       "      <td>400.0</td>\n",
       "      <td>523</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.742188</td>\n",
       "      <td>0.742188</td>\n",
       "      <td>512.0</td>\n",
       "      <td>002</td>\n",
       "      <td>M</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.625000</td>\n",
       "      <td>094127</td>\n",
       "      <td>250.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>060Y</td>\n",
       "      <td>888.0</td>\n",
       "      <td>20100101</td>\n",
       "      <td>3370.0</td>\n",
       "      <td>1</td>\n",
       "      <td>120.0</td>\n",
       "      <td>CT</td>\n",
       "      <td>/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...</td>\n",
       "      <td>1-0253-8</td>\n",
       "      <td>0.545455</td>\n",
       "      <td>0.596847</td>\n",
       "      <td>605.0</td>\n",
       "      <td>001</td>\n",
       "      <td>M</td>\n",
       "      <td>NaN</td>\n",
       "      <td>330.000000</td>\n",
       "      <td>094019</td>\n",
       "      <td>80.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    age  columns      date  exposure_time  files    kvp modality  \\\n",
       "0  057Y    888.0  20080101         4070.0      1  120.0       CT   \n",
       "1  057Y    512.0  20080101          400.0    131  120.0       CT   \n",
       "2  057Y    512.0  20080101          400.0    521  120.0       CT   \n",
       "3  057Y    512.0  20080101          400.0    131  120.0       CT   \n",
       "4  064Y    888.0  20140101         4075.0      1  120.0       CT   \n",
       "5  064Y    512.0  20140101          400.0    542  120.0       CT   \n",
       "6  064Y    512.0  20140101          400.0    136  120.0       CT   \n",
       "7  064Y    512.0  20140101          400.0    136  120.0       CT   \n",
       "8  060Y    512.0  20100101          400.0    523  120.0       CT   \n",
       "9  060Y    888.0  20100101         3370.0      1  120.0       CT   \n",
       "\n",
       "                                                path       pid  \\\n",
       "0  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "1  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "2  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "3  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "4  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "5  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "6  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "7  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "8  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "9  /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/S...  1-0253-8   \n",
       "\n",
       "   pixcel_spacing_1  pixcel_spacing_2   rows series sex  slice_spacing  \\\n",
       "0          0.545455          0.596847  733.0    001   M            NaN   \n",
       "1          0.683594          0.683594  512.0    002   M            NaN   \n",
       "2          0.683594          0.683594  512.0    004   M            NaN   \n",
       "3          0.683594          0.683594  512.0    003   M            NaN   \n",
       "4          0.545455          0.596847  734.0    001   M         10.000   \n",
       "5          0.703125          0.703125  512.0    002   M          0.625   \n",
       "6          0.703125          0.703125  512.0    004   M          0.625   \n",
       "7          0.703125          0.703125  512.0    003   M          0.625   \n",
       "8          0.742188          0.742188  512.0    002   M            NaN   \n",
       "9          0.545455          0.596847  605.0    001   M            NaN   \n",
       "\n",
       "   slice_thickness           time  x_ray_current  \n",
       "0       400.000000         081707           80.0  \n",
       "1         2.500000         081818          250.0  \n",
       "2         0.625000         081818          250.0  \n",
       "3         2.500000         081818          250.0  \n",
       "4       400.545454  120659.366914           80.0  \n",
       "5         0.625000  120749.620649          250.0  \n",
       "6         2.500000  120749.620649          250.0  \n",
       "7         2.500000  120749.620649          250.0  \n",
       "8         0.625000         094127          250.0  \n",
       "9       330.000000         094019           80.0  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dicom_profile_df.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(5882, 18)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dicom_profile_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "dicom_profile_df.to_csv('/pylon5/ac5616p/debdas/SCCORProcessing/SCCOR_dicom_profile.csv', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Dicom to Nifti"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/ /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20080628/001/\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "import sys\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "\n",
    "from preProcessUtils import copyfiles\n",
    "from preProcessUtils import run_dcm2niix\n",
    "\n",
    "def convert_dicom2niix(path,output_path):\n",
    "    \n",
    "    if not os.path.exists(path):\n",
    "        print(path,'not found!!!')\n",
    "        return False\n",
    "    \n",
    "    if not os.path.exists(output_path):\n",
    "        os.makedirs(output_path)          \n",
    "\n",
    "    niftiImageFile = os.path.join(output_path,path.split('/')[-1] + '.nii.gz')\n",
    "\n",
    "    if os.path.exists(niftiImageFile):\n",
    "        print(niftiImageFile,' found!!!')\n",
    "\n",
    "    dcm_tuple = (output_path,path)\n",
    "    run_dcm2niix(dcm_tuple)\n",
    "    \n",
    "    return True\n",
    "    \n",
    "def preProcessing(dicom_tuple):\n",
    "    path,output_path = dicom_tuple\n",
    "    convert_dicom2niix(path,output_path)\n",
    "\n",
    "\n",
    "\n",
    "path = '/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20080628/001/' #HB14229_CT_92148FC6_03_001_01_001.dcm\n",
    "output_path = '/home/debdas/SCCORProcessing/nifti/'\n",
    "\n",
    "complete = convert_dicom2niix(path,output_path)\n",
    "if not complete:\n",
    "    print('Can''t process {}.'.format(subj))\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import sys\n",
    "import glob\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "from datetime import datetime\n",
    "from multiprocessing import Pool\n",
    "import multiprocessing as mp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "starting_time = datetime.now()\n",
    "target_img_list = []\n",
    "run_parallel = True\n",
    "output_dir = '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/'\n",
    "image_io_df = pd.read_csv('/pylon5/ac5616p/debdas/SCCORProcessing/SCCOR_dicom_profile.csv')\n",
    "starting_index = 0\n",
    "ending_index = 1000\n",
    "image_rows = image_io_df.copy()\n",
    "#image_rows = image_io_df.iloc[starting_index:ending_index+1,:]\n",
    "image_rows = image_rows[image_rows['files'] > 0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "for index,row in image_rows.iterrows():\n",
    "    path = row['path']\n",
    "    output_path_ = row['path'].split('/')\n",
    "    output_path = output_path_[8]+'/'+output_path_[9]+'/'+output_path_[10]\n",
    "    output_path = output_dir + output_path\n",
    "\n",
    "    target_img_list.append((path,output_path))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0075-2/Date_20071215/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0075-2/Date_20071215/002'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0075-2/Date_20071215/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/003',\n",
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       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0166-2/Date_20100821/004'),\n",
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       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0166-2/Date_20100821/003'),\n",
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       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20080426/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0166-2/Date_20080426/001'),\n",
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       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0325-4/Date_20081108/003',\n",
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       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0325-4/Date_20081108/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0325-4/Date_20081108/004'),\n",
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       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0237-9/Date_20080531/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20080531/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0237-9/Date_20080531/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20080531/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0237-9/Date_20080531/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20080531/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0237-9/Date_20080531/002'),\n",
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       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20150221/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0377-9/Date_20150221/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20150221/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0377-9/Date_20110219/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20110219/002'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0377-9/Date_20110219/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20110219/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0377-9/Date_20110219/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20110219/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0377-9/Date_20110219/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20110219/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0377-9/Date_20090214/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20090214/002'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0377-9/Date_20090214/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20090214/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0377-9/Date_20090214/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20090214/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0377-9/Date_20090214/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0377-9/Date_20090214/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0706-5/Date_20120428/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0706-5/Date_20120428/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0706-5/Date_20120428/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0706-5/Date_20120428/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0706-5/Date_20120428/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0706-5/Date_20120428/002'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0706-5/Date_20120428/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0706-5/Date_20120428/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0706-5/Date_20100327/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0706-5/Date_20100327/002'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0706-5/Date_20100327/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0706-5/Date_20100327/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0706-5/Date_20100327/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0706-5/Date_20100327/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0706-5/Date_20100327/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0706-5/Date_20100327/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0628-3/Date_20091024/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0628-3/Date_20091024/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0628-3/Date_20091024/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0628-3/Date_20091024/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0628-3/Date_20091024/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0628-3/Date_20091024/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0628-3/Date_20091024/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0628-3/Date_20091024/002'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0026-2/Date_20070922/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0026-2/Date_20070922/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0026-2/Date_20070922/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0026-2/Date_20070922/002'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0026-2/Date_20070922/102',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0026-2/Date_20070922/102'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0026-2/Date_20070922/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0026-2/Date_20070922/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0026-2/Date_20070922/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0026-2/Date_20070922/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0042-9/Date_20071117/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0042-9/Date_20071117/002'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0042-9/Date_20071117/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0042-9/Date_20071117/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0042-9/Date_20071117/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0042-9/Date_20071117/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0042-9/Date_20071117/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0042-9/Date_20071117/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0246-0/Date_20080531/002',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0246-0/Date_20080531/002'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0246-0/Date_20080531/001',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0246-0/Date_20080531/001'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0246-0/Date_20080531/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0246-0/Date_20080531/004'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0246-0/Date_20080531/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0246-0/Date_20080531/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0246-0/Date_20101106/003',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0246-0/Date_20101106/003'),\n",
       " ('/pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0246-0/Date_20101106/004',\n",
       "  '/pylon5/ac5616p/debdas/SCCORProcessing/nifti/1-0246-0/Date_20101106/004'),\n",
       " ...]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "target_img_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5846"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(target_img_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "SCCOR_batch_df = pd.DataFrame(target_img_list)\n",
    "SCCOR_batch_df.to_csv('/pylon5/ac5616p/debdas/SCCORProcessing/SCCOR_batch_df.csv', index=False, header=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!dicom2niix.batch.py --csv-file-list /pylon5/ac5616p/debdas/SCCORProcessing/SCCOR_batch_df.csv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20080628/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20080628/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0712-0/Date_20120728/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20120728/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20141025/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20141025/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20090822/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20090822/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20140913/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20140913/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0712-0/Date_20120728/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20120728/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20090822/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20090822/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20110924/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20110924/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20090822/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20090822/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20141025/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20141025/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0712-0/Date_20100515/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20100515/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0712-0/Date_20100515/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20100515/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20080628/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20080628/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20141025/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20141025/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20141025/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20141025/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20080628/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20080628/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20100724/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20100724/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20140913/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20140913/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20080628/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20080628/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20110924/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20110924/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20100724/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20100724/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20140913/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20140913/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0712-0/Date_20120728/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20120728/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20100724/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20100724/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20110924/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20110924/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20140913/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20140913/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0253-8/Date_20100724/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20100724/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0712-0/Date_20100515/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20100515/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20110924/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20110924/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0712-0/Date_20120728/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20120728/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0712-0/Date_20100515/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20100515/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0584-5/Date_20090822/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20090822/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0214-7/Date_20080621/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0214-7/Date_20080621/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0214-7/Date_20080621/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0214-7/Date_20080621/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0214-7/Date_20080621/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0214-7/Date_20080621/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0214-7/Date_20080621/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0214-7/Date_20080621/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0659-0/Date_20091114/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0659-0/Date_20091114/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0659-0/Date_20091114/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0659-0/Date_20091114/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0659-0/Date_20091114/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0659-0/Date_20091114/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0659-0/Date_20091114/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0659-0/Date_20091114/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0190-5/Date_20080415/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0190-5/Date_20080415/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0190-5/Date_20080415/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0190-5/Date_20080415/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0659-0/Date_20091114/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20110924/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20090822/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20140913/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20141025/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20100515/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0075-2/Date_20071215/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0190-5/Date_20080415/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0190-5/Date_20080415/002\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0190-5/Date_20080415/102 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0190-5/Date_20080415/102\n",
      "/home/debdas/SCCORProcessing/nifti/1-0190-5/Date_20080415/001/001.nii.gz  found!!!\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0075-2/Date_20071215/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0075-2/Date_20071215/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0190-5/Date_20080415/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0190-5/Date_20080415/001\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0075-2/Date_20071215/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20140913/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0214-7/Date_20080621/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0166-2/Date_20100821/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20100821/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0166-2/Date_20100821/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20100821/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0166-2/Date_20100821/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20100821/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0166-2/Date_20100821/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20100821/001\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0190-5/Date_20080415/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0166-2/Date_20080426/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20080426/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0166-2/Date_20080426/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20080426/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20100821/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20100821/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0166-2/Date_20080426/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20080426/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0166-2/Date_20080426/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20080426/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0325-4/Date_20081108/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0325-4/Date_20081108/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0325-4/Date_20081108/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0325-4/Date_20081108/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0325-4/Date_20081108/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0325-4/Date_20081108/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0325-4/Date_20081108/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0325-4/Date_20081108/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20141025/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20120728/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0214-7/Date_20080621/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20080426/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20110924/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20080531/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20080531/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20080531/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20080531/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20080531/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20080531/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20080531/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20080531/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20100424/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20100424/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20100424/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20100424/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20080628/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0325-4/Date_20081108/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0659-0/Date_20091114/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20100724/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20100424/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20100424/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20100424/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20100424/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20140426/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20140426/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20140426/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20140426/001\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0712-0/Date_20100515/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20140426/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20140426/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0237-9/Date_20140426/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20140426/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0488-0/Date_20090410/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0488-0/Date_20090410/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0488-0/Date_20090410/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0488-0/Date_20090410/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20080531/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20140913/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0584-5/Date_20090822/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0488-0/Date_20090410/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0488-0/Date_20090410/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0488-0/Date_20090410/102 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0488-0/Date_20090410/102\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0488-0/Date_20090410/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0488-0/Date_20090410/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0318-2/Date_20080828/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0318-2/Date_20080828/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0318-2/Date_20080828/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0318-2/Date_20080828/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0318-2/Date_20080828/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0318-2/Date_20080828/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0318-2/Date_20080828/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0318-2/Date_20080828/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0318-2/Date_20080828/102 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0318-2/Date_20080828/102\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0208-1/Date_20080813/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0208-1/Date_20080813/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0208-1/Date_20080813/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0208-1/Date_20080813/004\n",
      "/home/debdas/SCCORProcessing/nifti/1-0208-1/Date_20080813/001/001.nii.gz  found!!!\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0208-1/Date_20080813/102 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0208-1/Date_20080813/102\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0208-1/Date_20080813/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0208-1/Date_20080813/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0208-1/Date_20080813/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0208-1/Date_20080813/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0318-2/Date_20080828/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20140426/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0075-2/Date_20071215/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0190-5/Date_20080415/102\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0440-8/Date_20090321/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0440-8/Date_20090321/001\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0440-8/Date_20090321/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0440-8/Date_20090321/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0440-8/Date_20090321/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0440-8/Date_20090321/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0440-8/Date_20090321/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0440-8/Date_20090321/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0441-5/Date_20090530/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0441-5/Date_20090530/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0441-5/Date_20090530/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0441-5/Date_20090530/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0441-5/Date_20090530/001 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0441-5/Date_20090530/001\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0488-0/Date_20090410/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0208-1/Date_20080813/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0208-1/Date_20080813/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0441-5/Date_20090530/102 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0441-5/Date_20090530/102\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0805-8/Date_20110316/003 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0805-8/Date_20110316/003\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0441-5/Date_20090530/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0441-5/Date_20090530/002\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0805-8/Date_20110316/004 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0805-8/Date_20110316/004\n",
      "dcm2niix -z i -f %f -o /home/debdas/SCCORProcessing/nifti/1-0805-8/Date_20110316/002 /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0805-8/Date_20110316/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20100724/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0253-8/Date_20100724/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0440-8/Date_20090321/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20100821/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0441-5/Date_20090530/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0325-4/Date_20081108/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0805-8/Date_20110316/003\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20080531/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0318-2/Date_20080828/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0441-5/Date_20090530/102\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0805-8/Date_20110316/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20100424/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0208-1/Date_20080813/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20080426/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0237-9/Date_20140426/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0488-0/Date_20090410/102\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0166-2/Date_20080426/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0440-8/Date_20090321/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0805-8/Date_20110316/002\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0208-1/Date_20080813/102\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0441-5/Date_20090530/004\n",
      "Failed to convert DICOM to NifTI: /pghbio/dbmi/batmanlab/Data/UPMC_Lung_Images/SCCOR/CT_Exams/1-0318-2/Date_20080828/102\n",
      "0 - 100: Time eclipsed: 0 hours 9 minuites 31 seconds\n"
     ]
    }
   ],
   "source": [
    "\n",
    "if len(target_img_list) > 0:\n",
    "\n",
    "    if run_parallel:\n",
    "\n",
    "        processes = mp.cpu_count()\n",
    "        pool = Pool(processes=processes)\n",
    "\n",
    "        # Calculate a good chunksize (based on implementation of pool.map)\n",
    "        chunksize, extra = divmod(len(target_img_list), 4 * processes)\n",
    "        if extra:\n",
    "            chunksize += 1\n",
    "\n",
    "        results = [result for result in pool.imap_unordered(preProcessing,\n",
    "                                            (img for img in target_img_list),\n",
    "                                            chunksize=chunksize)]\n",
    "\n",
    "        pool.close()\n",
    "        pool.join()\n",
    "\n",
    "    else:\n",
    "\n",
    "        for img in target_img_list:\n",
    "            convert_dicom2niix(img)\n",
    "\n",
    "ending_time = datetime.now()\n",
    "\n",
    "time_eclipsed = ending_time - starting_time\n",
    "minutes = divmod(time_eclipsed.seconds,60)\n",
    "hours = divmod(minutes[0],60) \n",
    "print('{} - {}: Time eclipsed: {} hours {} minuites {} seconds'.format(\n",
    "                        starting_index,ending_index,hours[0],hours[1],minutes[1]))"
   ]
  }
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