BIDS HW .ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "<ipython-input-1-d143d577da25>:4: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment\n",
      "Please use with caution.  We would be grateful for your help in improving them\n",
      "  import nibabel.nicom.csareader\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "Dataset.file_meta -------------------------------\n",
       "(0002, 0000) File Meta Information Group Length  UL: 202\n",
       "(0002, 0001) File Meta Information Version       OB: b'\\x00\\x01'\n",
       "(0002, 0002) Media Storage SOP Class UID         UI: MR Image Storage\n",
       "(0002, 0003) Media Storage SOP Instance UID      UI: 1.3.12.2.1107.5.2.43.166003.201906191526379774213981\n",
       "(0002, 0010) Transfer Syntax UID                 UI: Explicit VR Little Endian\n",
       "(0002, 0012) Implementation Class UID            UI: 1.2.40.0.13.1.1\n",
       "(0002, 0013) Implementation Version Name         SH: 'dcm4che-2.0'\n",
       "(0002, 0016) Source Application Entity Title     AE: 'AN_MEDCOMNT204'\n",
       "-------------------------------------------------\n",
       "(0008, 0005) Specific Character Set              CS: 'ISO_IR 100'\n",
       "(0008, 0008) Image Type                          CS: ['ORIGINAL', 'PRIMARY', 'M', 'ND']\n",
       "(0008, 0012) Instance Creation Date              DA: '20190619'\n",
       "(0008, 0013) Instance Creation Time              TM: '152641.528000'\n",
       "(0008, 0016) SOP Class UID                       UI: MR Image Storage\n",
       "(0008, 0018) SOP Instance UID                    UI: 1.3.12.2.1107.5.2.43.166003.201906191526379774213981\n",
       "(0008, 0020) Study Date                          DA: '20190619'\n",
       "(0008, 0021) Series Date                         DA: '20190619'\n",
       "(0008, 0022) Acquisition Date                    DA: '20190619'\n",
       "(0008, 0023) Content Date                        DA: '20190619'\n",
       "(0008, 0030) Study Time                          TM: '150037.662000'\n",
       "(0008, 0031) Series Time                         TM: '152641.517000'\n",
       "(0008, 0032) Acquisition Time                    TM: '152635.057500'\n",
       "(0008, 0033) Content Time                        TM: '152641.528000'\n",
       "(0008, 0050) Accession Number                    SH: ''\n",
       "(0008, 0060) Modality                            CS: 'MR'\n",
       "(0008, 0070) Manufacturer                        LO: 'SIEMENS'\n",
       "(0008, 0080) Institution Name                    LO: 'FIU Center For Imaging Science'\n",
       "(0008, 0081) Institution Address                 ST: 'SW 8TH ST, OE116 11200,MIAMI,Med-Lab,US,33199'\n",
       "(0008, 0090) Referring Physician's Name          PN: ''\n",
       "(0008, 1010) Station Name                        SH: 'AWP166003'\n",
       "(0008, 1030) Study Description                   LO: 'Mattfeld_REVL'\n",
       "(0008, 103e) Series Description                  LO: 'fMRI_DistortionMap_PA'\n",
       "(0008, 1040) Institutional Department Name       LO: 'Department'\n",
       "(0008, 1050) Performing Physician's Name         PN: ''\n",
       "(0008, 1070) Operators' Name                     PN: 'RR'\n",
       "(0008, 1090) Manufacturer's Model Name           LO: 'Prisma'\n",
       "(0008, 1140)  Referenced Image Sequence   3 item(s) ---- \n",
       "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
       "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915162823169893758\n",
       "   ---------\n",
       "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
       "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915241050432013699\n",
       "   ---------\n",
       "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
       "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915163172628493761\n",
       "   ---------\n",
       "(0010, 0010) Patient's Name                      PN: 'Mattfeld_REVL-000-vCAT-021'\n",
       "(0010, 0020) Patient ID                          LO: 'Mattfeld_REVL-000-vCAT-021-S1'\n",
       "(0010, 0030) Patient's Birth Date                DA: '19770101'\n",
       "(0010, 0040) Patient's Sex                       CS: 'M'\n",
       "(0010, 1010) Patient's Age                       AS: '042Y'\n",
       "(0010, 1020) Patient's Size                      DS: \"1.82880366\"\n",
       "(0010, 1030) Patient's Weight                    DS: \"84.3681915522\"\n",
       "(0010, 4000) Patient Comments                    LT: 'Project: Mattfeld_REVL;Mattfeld_REVL-000-vCAT-021 ; Session: Mattfeld_REVL-000-vCAT-021-S1'\n",
       "(0012, 0064)  De-identification Method Code Sequence   1 item(s) ---- \n",
       "   (0008, 0100) Code Value                          SH: '2'\n",
       "   (0008, 0102) Coding Scheme Designator            SH: 'XNAT'\n",
       "   (0008, 0103) Coding Scheme Version               SH: '0.1'\n",
       "   (0008, 0104) Code Meaning                        LO: 'XNAT Edit Script'\n",
       "   ---------\n",
       "(0018, 0015) Body Part Examined                  CS: 'BRAIN'\n",
       "(0018, 0020) Scanning Sequence                   CS: 'EP'\n",
       "(0018, 0021) Sequence Variant                    CS: ['SK', 'SP']\n",
       "(0018, 0022) Scan Options                        CS: 'FS'\n",
       "(0018, 0023) MR Acquisition Type                 CS: '2D'\n",
       "(0018, 0024) Sequence Name                       SH: 'epse2d1_100'\n",
       "(0018, 0025) Angio Flag                          CS: 'N'\n",
       "(0018, 0050) Slice Thickness                     DS: \"2.0\"\n",
       "(0018, 0080) Repetition Time                     DS: \"6720.0\"\n",
       "(0018, 0081) Echo Time                           DS: \"80.0\"\n",
       "(0018, 0083) Number of Averages                  DS: \"1.0\"\n",
       "(0018, 0084) Imaging Frequency                   DS: \"123.249135\"\n",
       "(0018, 0085) Imaged Nucleus                      SH: '1H'\n",
       "(0018, 0086) Echo Number(s)                      IS: \"1\"\n",
       "(0018, 0087) Magnetic Field Strength             DS: \"3.0\"\n",
       "(0018, 0088) Spacing Between Slices              DS: \"2.0\"\n",
       "(0018, 0089) Number of Phase Encoding Steps      IS: \"99\"\n",
       "(0018, 0091) Echo Train Length                   IS: \"25\"\n",
       "(0018, 0093) Percent Sampling                    DS: \"100.0\"\n",
       "(0018, 0094) Percent Phase Field of View         DS: \"100.0\"\n",
       "(0018, 0095) Pixel Bandwidth                     DS: \"2780.0\"\n",
       "(0018, 1000) Device Serial Number                LO: '166003'\n",
       "(0018, 1020) Software Versions                   LO: 'syngo MR E11'\n",
       "(0018, 1030) Protocol Name                       LO: 'fMRI_DistortionMap_PA'\n",
       "(0018, 1251) Transmit Coil Name                  SH: 'Body'\n",
       "(0018, 1310) Acquisition Matrix                  US: [100, 0, 0, 100]\n",
       "(0018, 1312) In-plane Phase Encoding Direction   CS: 'COL'\n",
       "(0018, 1314) Flip Angle                          DS: \"90.0\"\n",
       "(0018, 1315) Variable Flip Angle Flag            CS: 'N'\n",
       "(0018, 1316) SAR                                 DS: \"0.06979007957516\"\n",
       "(0018, 1318) dB/dt                               DS: \"0.0\"\n",
       "(0018, 5100) Patient Position                    CS: 'HFS'\n",
       "(0019, 0010) Private Creator                     LO: 'SIEMENS MR HEADER'\n",
       "(0019, 1008) [CSA Image Header Type]             CS: 'IMAGE NUM 4'\n",
       "(0019, 1009) [CSA Image Header Version ??]       LO: '1.0'\n",
       "(0019, 100b) [SliceMeasurementDuration]          DS: \"19000.0\"\n",
       "(0019, 100f) [GradientMode]                      SH: ''\n",
       "(0019, 1011) [FlowCompensation]                  SH: 'No'\n",
       "(0019, 1012) [TablePositionOrigin]               SL: [0, 0, -1306]\n",
       "(0019, 1013) [ImaAbsTablePosition]               SL: [0, 0, -1306]\n",
       "(0019, 1014) [ImaRelTablePosition]               IS: [0, 0, 0]\n",
       "(0019, 1015) [SlicePosition_PCS]                 FD: [-101.7710135, -121.23502083, 18.39929037]\n",
       "(0019, 1016) [TimeAfterStart]                    DS: \"0.555\"\n",
       "(0019, 1017) [SliceResolution]                   DS: \"1.0\"\n",
       "(0019, 1018) [RealDwellTime]                     IS: \"1800\"\n",
       "(0019, 1028) [BandwidthPerPixelPhaseEncode]      FD: 71.429\n",
       "(0020, 000d) Study Instance UID                  UI: 1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017\n",
       "(0020, 000e) Series Instance UID                 UI: 1.3.12.2.1107.5.2.43.166003.2019061915261893767113930.0.0.0\n",
       "(0020, 0010) Study ID                            SH: '1'\n",
       "(0020, 0011) Series Number                       IS: \"6\"\n",
       "(0020, 0012) Acquisition Number                  IS: \"1\"\n",
       "(0020, 0013) Instance Number                     IS: \"8\"\n",
       "(0020, 0032) Image Position (Patient)            DS: [-101.77101349831, -121.23502083227, 18.399290374983]\n",
       "(0020, 0037) Image Orientation (Patient)         DS: [1, 0, 0, 0, 0.86602540210929, -0.5000000029014]\n",
       "(0020, 0052) Frame of Reference UID              UI: 1.3.12.2.1107.5.2.43.166003.1.20190619151307196.0.0.0\n",
       "(0020, 1040) Position Reference Indicator        LO: ''\n",
       "(0020, 1041) Slice Location                      DS: \"-44.683257922369\"\n",
       "(0028, 0002) Samples per Pixel                   US: 1\n",
       "(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'\n",
       "(0028, 0010) Rows                                US: 100\n",
       "(0028, 0011) Columns                             US: 100\n",
       "(0028, 0030) Pixel Spacing                       DS: [2, 2]\n",
       "(0028, 0100) Bits Allocated                      US: 16\n",
       "(0028, 0101) Bits Stored                         US: 12\n",
       "(0028, 0102) High Bit                            US: 11\n",
       "(0028, 0103) Pixel Representation                US: 0\n",
       "(0028, 0106) Smallest Image Pixel Value          US: 0\n",
       "(0028, 0107) Largest Image Pixel Value           US: 2414\n",
       "(0028, 1050) Window Center                       DS: \"503.0\"\n",
       "(0028, 1051) Window Width                        DS: \"1127.0\"\n",
       "(0028, 1055) Window Center & Width Explanation   LO: 'Algo1'\n",
       "(0029, 0010) Private Creator                     LO: 'SIEMENS CSA HEADER'\n",
       "(0029, 0011) Private Creator                     LO: 'SIEMENS MEDCOM HEADER'\n",
       "(0029, 0012) Private Creator                     LO: 'SIEMENS MEDCOM HEADER2'\n",
       "(0029, 1008) [CSA Image Header Type]             CS: 'IMAGE NUM 4'\n",
       "(0029, 1009) [CSA Image Header Version]          LO: '20190619'\n",
       "(0029, 1010) [CSA Image Header Info]             OB: Array of 11240 elements\n",
       "(0029, 1018) [CSA Series Header Type]            CS: 'MR'\n",
       "(0029, 1019) [CSA Series Header Version]         LO: '20190619'\n",
       "(0029, 1020) [CSA Series Header Info]            OB: Array of 144316 elements\n",
       "(0029, 1120) [MedCom History Information]        OB: Array of 308 elements\n",
       "(0029, 1260) [Series Workflow Status]            LO: 'com'\n",
       "(0040, 0244) Performed Procedure Step Start Date DA: '20190619'\n",
       "(0040, 0245) Performed Procedure Step Start Time TM: '150037.732000'\n",
       "(0040, 0253) Performed Procedure Step ID         SH: 'MR20190619150037'\n",
       "(0040, 0254) Performed Procedure Step Descriptio LO: 'Mattfeld_REVL^Mattfeld_REVL'\n",
       "(0040, 0280) Comments on the Performed Procedure ST: ''\n",
       "(0051, 0010) Private Creator                     LO: 'SIEMENS MR HEADER'\n",
       "(0051, 1008) [CSA Image Header Type]             CS: 'IMAGE NUM 4'\n",
       "(0051, 1009) [CSA Image Header Version ??]       LO: '1.0'\n",
       "(0051, 100a) [Unknown]                           LO: 'TA 19.00'\n",
       "(0051, 100b) [AcquisitionMatrixText]             LO: '100*100'\n",
       "(0051, 100c) [Unknown]                           LO: 'FoV 200*200'\n",
       "(0051, 100d) [Unknown]                           SH: 'SP F44.7'\n",
       "(0051, 100e) [Unknown]                           LO: 'Tra>Cor(-30.0)'\n",
       "(0051, 100f) [CoilString]                        LO: 'HEA;HEP'\n",
       "(0051, 1011) [PATModeText]                       LO: 'p4'\n",
       "(0051, 1012) [Unknown]                           SH: 'TP 0'\n",
       "(0051, 1013) [PositivePCSDirections]             SH: '+LPH'\n",
       "(0051, 1016) [Unknown]                           LO: 'p4 M/ND'\n",
       "(0051, 1017) [Unknown]                           SH: 'SL 2.0'\n",
       "(0051, 1019) [Unknown]                           LO: 'A1/FS'\n",
       "(7fe0, 0010) Pixel Data                          OW: Array of 20000 elements"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from glob import glob\n",
    "from pydicom import dcmread\n",
    "import os.path\n",
    "import nibabel.nicom.csareader\n",
    "import pandas as pd\n",
    "dir = '/Users/donishasmith/'\n",
    "scans = glob(os.path.join(dir, 'Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/*'))\n",
    "study1 = dcmread(scans[1])\n",
    "study1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'TR # = 66'} {'TR = 6720 ms'} {'TE = 80 ms'} {'Acquisition Matrix = [100, 0, 0, 100]'} {'Flip angle = 90 '} {'Acquisition Number = 1'} {'Protocol name = fMRI_DistortionMap_PA'} {'In-plane Phase Encoding Direction = COL'} {'Phase Encoding Direction = 0, 1 = +; 0 = -, COL, 1 = PA; COL, 0 = AP'} {'Field of View = FoV 200*200'}\n"
     ]
    }
   ],
   "source": [
    "enc = nibabel.nicom.csareader.read(study1[int('00291010',16)].value)\n",
    "#\"Slice times([MosaicRefAcqTimes]) = {} \" .format(study1[int(\"00191029\",16)].value)},\n",
    "info = print({\"TR # = {}\" .format(len(scans))},\n",
    "             {\"TR = {} ms\" .format(study1.RepetitionTime)},\n",
    "             {\"TE = {} ms\" .format(study1.EchoTime)},\n",
    "             {\"Acquisition Matrix = {}\" .format(study1.AcquisitionMatrix)},\n",
    "             {\"Flip angle = {} \" .format(study1.FlipAngle)},\n",
    "             {\"Acquisition Number = {}\" .format(study1.AcquisitionNumber)},\n",
    "             {\"Protocol name = {}\" .format(study1.SeriesDescription)},\n",
    "             {\"In-plane Phase Encoding Direction = {}\" .format(study1[int('00181312',16)].value)},\n",
    "             {\"Phase Encoding Direction = {}, 1 = +; 0 = -, COL, 1 = PA; COL, 0 = AP\".format(enc['tags']['PhaseEncodingDirectionPositive']['items'][0])},\n",
    "             {\"Field of View = {}\" .format(study1[int(\"0051100c\",16)].value)})\n",
    "info"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>series_id</th>\n",
       "      <th>series_files</th>\n",
       "      <th>dim1</th>\n",
       "      <th>dim2</th>\n",
       "      <th>dim3</th>\n",
       "      <th>dim4</th>\n",
       "      <th>series_description</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1-localizer_32ch</td>\n",
       "      <td>3</td>\n",
       "      <td>512</td>\n",
       "      <td>512</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>localizer_32ch</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2-T1w_MPR_vNav_setter</td>\n",
       "      <td>32</td>\n",
       "      <td>32</td>\n",
       "      <td>32</td>\n",
       "      <td>32</td>\n",
       "      <td>1</td>\n",
       "      <td>T1w_MPR_vNav_setter</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3-T1w_MPR_vNav</td>\n",
       "      <td>145</td>\n",
       "      <td>32</td>\n",
       "      <td>32</td>\n",
       "      <td>32</td>\n",
       "      <td>145</td>\n",
       "      <td>T1w_MPR_vNav_setter</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4-T1w_MPR_vNav</td>\n",
       "      <td>176</td>\n",
       "      <td>256</td>\n",
       "      <td>256</td>\n",
       "      <td>176</td>\n",
       "      <td>1</td>\n",
       "      <td>T1w_MPR_vNav</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5-T1w_MPR_vNav</td>\n",
       "      <td>176</td>\n",
       "      <td>256</td>\n",
       "      <td>256</td>\n",
       "      <td>176</td>\n",
       "      <td>1</td>\n",
       "      <td>T1w_MPR_vNav</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>6-fMRI_DistortionMap_PA</td>\n",
       "      <td>66</td>\n",
       "      <td>100</td>\n",
       "      <td>100</td>\n",
       "      <td>66</td>\n",
       "      <td>1</td>\n",
       "      <td>fMRI_DistortionMap_PA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>7-fMRI_DistortionMap_AP</td>\n",
       "      <td>66</td>\n",
       "      <td>100</td>\n",
       "      <td>100</td>\n",
       "      <td>66</td>\n",
       "      <td>1</td>\n",
       "      <td>fMRI_DistortionMap_AP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>8-fMRI_REVL_ROI_loc_1</td>\n",
       "      <td>304</td>\n",
       "      <td>100</td>\n",
       "      <td>100</td>\n",
       "      <td>66</td>\n",
       "      <td>304</td>\n",
       "      <td>fMRI_REVL_ROI_loc_1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>9-fMRI_REVL_ROI_loc_2</td>\n",
       "      <td>304</td>\n",
       "      <td>100</td>\n",
       "      <td>100</td>\n",
       "      <td>66</td>\n",
       "      <td>304</td>\n",
       "      <td>fMRI_REVL_ROI_loc_2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>10-fMRI_REVL_Study_1</td>\n",
       "      <td>355</td>\n",
       "      <td>100</td>\n",
       "      <td>100</td>\n",
       "      <td>66</td>\n",
       "      <td>355</td>\n",
       "      <td>fMRI_REVL_Study_1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>11-fMRI_REVL_Study_2</td>\n",
       "      <td>355</td>\n",
       "      <td>100</td>\n",
       "      <td>100</td>\n",
       "      <td>66</td>\n",
       "      <td>355</td>\n",
       "      <td>fMRI_REVL_Study_2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>12-fMRI_REVL_Study_3</td>\n",
       "      <td>355</td>\n",
       "      <td>100</td>\n",
       "      <td>100</td>\n",
       "      <td>66</td>\n",
       "      <td>355</td>\n",
       "      <td>fMRI_REVL_Study_3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>13-fMRI_REVL_Study_4</td>\n",
       "      <td>355</td>\n",
       "      <td>100</td>\n",
       "      <td>100</td>\n",
       "      <td>66</td>\n",
       "      <td>355</td>\n",
       "      <td>fMRI_REVL_Study_4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>14-dMRI_DistortionMap_AP_dMRI_REVL</td>\n",
       "      <td>81</td>\n",
       "      <td>140</td>\n",
       "      <td>140</td>\n",
       "      <td>81</td>\n",
       "      <td>1</td>\n",
       "      <td>dMRI_DistortionMap_AP_dMRI_REVL</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>15-dMRI_DistortionMap_PA_dMRI_REVL</td>\n",
       "      <td>81</td>\n",
       "      <td>140</td>\n",
       "      <td>140</td>\n",
       "      <td>81</td>\n",
       "      <td>1</td>\n",
       "      <td>dMRI_DistortionMap_PA_dMRI_REVL</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>16-dMRI_AP_REVL</td>\n",
       "      <td>103</td>\n",
       "      <td>140</td>\n",
       "      <td>140</td>\n",
       "      <td>81</td>\n",
       "      <td>103</td>\n",
       "      <td>dMRI_AP_REVL</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                             series_id  series_files  dim1  dim2  dim3  dim4  \\\n",
       "0                     1-localizer_32ch             3   512   512     3     1   \n",
       "1                2-T1w_MPR_vNav_setter            32    32    32    32     1   \n",
       "2                       3-T1w_MPR_vNav           145    32    32    32   145   \n",
       "3                       4-T1w_MPR_vNav           176   256   256   176     1   \n",
       "4                       5-T1w_MPR_vNav           176   256   256   176     1   \n",
       "5              6-fMRI_DistortionMap_PA            66   100   100    66     1   \n",
       "6              7-fMRI_DistortionMap_AP            66   100   100    66     1   \n",
       "7                8-fMRI_REVL_ROI_loc_1           304   100   100    66   304   \n",
       "8                9-fMRI_REVL_ROI_loc_2           304   100   100    66   304   \n",
       "9                 10-fMRI_REVL_Study_1           355   100   100    66   355   \n",
       "10                11-fMRI_REVL_Study_2           355   100   100    66   355   \n",
       "11                12-fMRI_REVL_Study_3           355   100   100    66   355   \n",
       "12                13-fMRI_REVL_Study_4           355   100   100    66   355   \n",
       "13  14-dMRI_DistortionMap_AP_dMRI_REVL            81   140   140    81     1   \n",
       "14  15-dMRI_DistortionMap_PA_dMRI_REVL            81   140   140    81     1   \n",
       "15                     16-dMRI_AP_REVL           103   140   140    81   103   \n",
       "\n",
       "                 series_description  \n",
       "0                    localizer_32ch  \n",
       "1               T1w_MPR_vNav_setter  \n",
       "2               T1w_MPR_vNav_setter  \n",
       "3                      T1w_MPR_vNav  \n",
       "4                      T1w_MPR_vNav  \n",
       "5             fMRI_DistortionMap_PA  \n",
       "6             fMRI_DistortionMap_AP  \n",
       "7               fMRI_REVL_ROI_loc_1  \n",
       "8               fMRI_REVL_ROI_loc_2  \n",
       "9                 fMRI_REVL_Study_1  \n",
       "10                fMRI_REVL_Study_2  \n",
       "11                fMRI_REVL_Study_3  \n",
       "12                fMRI_REVL_Study_4  \n",
       "13  dMRI_DistortionMap_AP_dMRI_REVL  \n",
       "14  dMRI_DistortionMap_PA_dMRI_REVL  \n",
       "15                     dMRI_AP_REVL  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#heudiconv -d '/Users/donishasmith/Mattfeld_REVL-000-vCAT-{subject}-S1/*/*/*/*/*/*' -s 021 -f '/Users/donishasmith/mattfeld_2020/psb6351_heuristic.py' -c none  -o '/Users/donishasmith/heudiconv'\n",
    "\n",
    "path2info_file = os.path.join(dir, 'heudiconv/.heudiconv/021/info')\n",
    "dicominfo_df = pd.read_csv(path2info_file + '/dicominfo.tsv', sep=\"\\t\")\n",
    "limited_dicominfo_df = dicominfo_df[['series_id', 'series_files', 'dim1', 'dim2', 'dim3', 'dim4', 'series_description']]\n",
    "\n",
    "limited_dicominfo_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['total_files_till_now', 'example_dcm_file', 'series_id', 'dcm_dir_name',\n",
       "       'series_files', 'unspecified', 'dim1', 'dim2', 'dim3', 'dim4', 'TR',\n",
       "       'TE', 'protocol_name', 'is_motion_corrected', 'is_derived',\n",
       "       'patient_id', 'study_description', 'referring_physician_name',\n",
       "       'series_description', 'sequence_name', 'image_type', 'accession_number',\n",
       "       'patient_age', 'patient_sex', 'date', 'series_uid'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dicominfo_df.keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "environ{'ALLUSERSPROFILE': 'C:\\\\ProgramData',\n",
       "        'APPDATA': 'C:\\\\Users\\\\Patricio Viera\\\\AppData\\\\Roaming',\n",
       "        'COMMONPROGRAMFILES': 'C:\\\\Program Files\\\\Common Files',\n",
       "        'COMMONPROGRAMFILES(X86)': 'C:\\\\Program Files (x86)\\\\Common Files',\n",
       "        'COMMONPROGRAMW6432': 'C:\\\\Program Files\\\\Common Files',\n",
       "        'COMPUTERNAME': 'LAPTOP-0V2HBC0L',\n",
       "        'COMSPEC': 'C:\\\\WINDOWS\\\\system32\\\\cmd.exe',\n",
       "        'DRIVERDATA': 'C:\\\\Windows\\\\System32\\\\Drivers\\\\DriverData',\n",
       "        'EMC_AUTOPLAY': 'C:\\\\Program Files (x86)\\\\Common Files\\\\Roxio Shared\\\\',\n",
       "        'FPS_BROWSER_APP_PROFILE_STRING': 'Internet Explorer',\n",
       "        'FPS_BROWSER_USER_PROFILE_STRING': 'Default',\n",
       "        'HOMEDRIVE': 'C:',\n",
       "        'HOMEPATH': '\\\\Users\\\\Patricio Viera',\n",
       "        'LOCALAPPDATA': 'C:\\\\Users\\\\Patricio Viera\\\\AppData\\\\Local',\n",
       "        'LOGONSERVER': '\\\\\\\\LAPTOP-0V2HBC0L',\n",
       "        'NUMBER_OF_PROCESSORS': '8',\n",
       "        'ONEDRIVE': 'C:\\\\Users\\\\Patricio Viera\\\\OneDrive',\n",
       "        'ONEDRIVECONSUMER': 'C:\\\\Users\\\\Patricio Viera\\\\OneDrive',\n",
       "        'OS': 'Windows_NT',\n",
       "        'PATH': 'C:\\\\Users\\\\Patricio Viera\\\\Anaconda3;C:\\\\Users\\\\Patricio Viera\\\\Anaconda3\\\\Library\\\\mingw-w64\\\\bin;C:\\\\Users\\\\Patricio Viera\\\\Anaconda3\\\\Library\\\\usr\\\\bin;C:\\\\Users\\\\Patricio Viera\\\\Anaconda3\\\\Library\\\\bin;C:\\\\Users\\\\Patricio Viera\\\\Anaconda3\\\\Scripts;C:\\\\Program Files (x86)\\\\NICE\\\\DCV\\\\bin64;C:\\\\Program Files (x86)\\\\NICE\\\\DCV\\\\bin;C:\\\\Windows\\\\system32;C:\\\\Windows;C:\\\\Windows\\\\System32\\\\Wbem;C:\\\\Windows\\\\System32\\\\WindowsPowerShell\\\\v1.0\\\\;C:\\\\Windows\\\\System32\\\\OpenSSH\\\\;C:\\\\Program Files (x86)\\\\NVIDIA Corporation\\\\PhysX\\\\Common;C:\\\\Program Files\\\\NVIDIA Corporation\\\\NVIDIA NvDLISR;C:\\\\WINDOWS\\\\system32;C:\\\\WINDOWS;C:\\\\WINDOWS\\\\System32\\\\Wbem;C:\\\\WINDOWS\\\\System32\\\\WindowsPowerShell\\\\v1.0\\\\;C:\\\\WINDOWS\\\\System32\\\\OpenSSH\\\\;C:\\\\Program Files (x86)\\\\Common Files\\\\Roxio Shared\\\\DLLShared\\\\;C:\\\\Program Files (x86)\\\\Common Files\\\\Roxio Shared\\\\DLLShared\\\\;C:\\\\Program Files (x86)\\\\Common Files\\\\Roxio Shared\\\\Game1X\\\\DLLShared\\\\;C:\\\\Users\\\\Patricio;C:\\\\Program Files\\\\Git\\\\cmd;C:\\\\Users\\\\Patricio Viera\\\\anaconda3;C:\\\\Users\\\\Patricio Viera\\\\anaconda3\\\\Library\\\\mingw-w64\\\\bin;C:\\\\Users\\\\Patricio Viera\\\\anaconda3\\\\Library\\\\usr\\\\bin;C:\\\\Users\\\\Patricio Viera\\\\anaconda3\\\\Library\\\\bin;C:\\\\Users\\\\Patricio Viera\\\\anaconda3\\\\Scripts;C:\\\\Users\\\\Patricio Viera\\\\AppData\\\\Local\\\\Microsoft\\\\WindowsApps;C:\\\\Users\\\\Patricio Viera\\\\AppData\\\\Local\\\\GitHubDesktop\\\\bin;C:\\\\Users\\\\Patricio Viera\\\\AppData\\\\Local\\\\atom\\\\bin;C:\\\\Users\\\\Patricio Viera\\\\AppData\\\\Local\\\\Microsoft\\\\WindowsApps',\n",
       "        'PATHEXT': '.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC',\n",
       "        'PROCESSOR_ARCHITECTURE': 'AMD64',\n",
       "        'PROCESSOR_IDENTIFIER': 'AMD64 Family 23 Model 24 Stepping 1, AuthenticAMD',\n",
       "        'PROCESSOR_LEVEL': '23',\n",
       "        'PROCESSOR_REVISION': '1801',\n",
       "        'PROGRAMDATA': 'C:\\\\ProgramData',\n",
       "        'PROGRAMFILES': 'C:\\\\Program Files',\n",
       "        'PROGRAMFILES(X86)': 'C:\\\\Program Files (x86)',\n",
       "        'PROGRAMW6432': 'C:\\\\Program Files',\n",
       "        'PSMODULEPATH': 'C:\\\\Program Files\\\\WindowsPowerShell\\\\Modules;C:\\\\WINDOWS\\\\system32\\\\WindowsPowerShell\\\\v1.0\\\\Modules',\n",
       "        'PUBLIC': 'C:\\\\Users\\\\Public',\n",
       "        'SESSIONNAME': 'Console',\n",
       "        'SYSTEMDRIVE': 'C:',\n",
       "        'SYSTEMROOT': 'C:\\\\WINDOWS',\n",
       "        'TEMP': 'C:\\\\Users\\\\PATRIC~1\\\\AppData\\\\Local\\\\Temp',\n",
       "        'TMP': 'C:\\\\Users\\\\PATRIC~1\\\\AppData\\\\Local\\\\Temp',\n",
       "        'USERDOMAIN': 'LAPTOP-0V2HBC0L',\n",
       "        'USERDOMAIN_ROAMINGPROFILE': 'LAPTOP-0V2HBC0L',\n",
       "        'USERNAME': 'Patricio Viera',\n",
       "        'USERPROFILE': 'C:\\\\Users\\\\Patricio Viera',\n",
       "        'WINDIR': 'C:\\\\WINDOWS',\n",
       "        'CONDA_PREFIX': 'C:\\\\Users\\\\Patricio Viera\\\\Anaconda3',\n",
       "        'KERNEL_LAUNCH_TIMEOUT': '40',\n",
       "        'JPY_INTERRUPT_EVENT': '2320',\n",
       "        'IPY_INTERRUPT_EVENT': '2320',\n",
       "        'JPY_PARENT_PID': '2200',\n",
       "        'TERM': 'xterm-color',\n",
       "        'CLICOLOR': '1',\n",
       "        'PAGER': 'cat',\n",
       "        'GIT_PAGER': 'cat',\n",
       "        'MPLBACKEND': 'module://ipykernel.pylab.backend_inline'}"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os\n",
    "os.environ"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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