Read_Dicom_Headers.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 102,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "# Import necessary modules\n",
    "# glob allows unix style pathname pattern expansion\n",
    "from glob import glob\n",
    "# pydicom is the python dicom reader\n",
    "import pydicom as dicom"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "# 5-T1w_MPR_vNav -- MPRAGE structrual dicoms\n",
    "\n",
    "# directories will have to be specific to your computer\n",
    "base_dir = '/Users/emusser/Documents/GitHub'\n",
    "proj_dir = '/mattfeld_2020/code'\n",
    "subj_dir = '/Mattfeld_REVL-000-vCAT-021-S1/scans/5-T1w_MPR_vNav/resources/DICOM/files/'\n",
    "\n",
    "# with strings I can concatenate them with simple addition lines\n",
    "data_dir = base_dir + proj_dir + subj_dir\n",
    "\n",
    "\n",
    "# Here I use glob to grab the dicom files\n",
    "# Why would I use glob?  What does it give me?\n",
    "data_files = glob(data_dir + '/*')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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'/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/5-T1w_MPR_vNav/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-5-87-yul9n7.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/5-T1w_MPR_vNav/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-5-53-10tbmsk.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/5-T1w_MPR_vNav/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-5-90-lsosa8.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/5-T1w_MPR_vNav/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-5-56-hbhekf.dcm']\n"
     ]
    }
   ],
   "source": [
    "print(data_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Here I am using the python dicom reader to read in a dicom header\n",
    "# What should go between the square brackets []\n",
    "data_set = dicom.dcmread(data_files[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dataset.file_meta -------------------------------\n",
      "(0002, 0000) File Meta Information Group Length  UL: 204\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: 1.3.12.2.1107.5.2.43.166003.2019061915241161003513836\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', 'NORM']\n",
      "(0008, 0012) Instance Creation Date              DA: '20190619'\n",
      "(0008, 0013) Instance Creation Time              TM: '152413.677000'\n",
      "(0008, 0016) SOP Class UID                       UI: MR Image Storage\n",
      "(0008, 0018) SOP Instance UID                    UI: 1.3.12.2.1107.5.2.43.166003.2019061915241161003513836\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: '152413.328000'\n",
      "(0008, 0032) Acquisition Time                    TM: '151756.262500'\n",
      "(0008, 0033) Content Time                        TM: '152413.677000'\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: 'T1w_MPR_vNav'\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: 1.3.12.2.1107.5.2.43.166003.2019061915163521984993764\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",
      "   (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",
      "(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: ['GR', 'IR']\n",
      "(0018, 0021) Sequence Variant                    CS: ['SK', 'SP', 'MP']\n",
      "(0018, 0022) Scan Options                        CS: ['IR', 'WE']\n",
      "(0018, 0023) MR Acquisition Type                 CS: '3D'\n",
      "(0018, 0024) Sequence Name                       SH: 'tfl3d1_16ns'\n",
      "(0018, 0025) Angio Flag                          CS: 'N'\n",
      "(0018, 0050) Slice Thickness                     DS: \"1.0\"\n",
      "(0018, 0080) Repetition Time                     DS: \"2500.0\"\n",
      "(0018, 0081) Echo Time                           DS: \"2.9\"\n",
      "(0018, 0082) Inversion Time                      DS: \"1070.0\"\n",
      "(0018, 0083) Number of Averages                  DS: \"1.0\"\n",
      "(0018, 0084) Imaging Frequency                   DS: \"123.249149\"\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, 0089) Number of Phase Encoding Steps      IS: \"255\"\n",
      "(0018, 0091) Echo Train Length                   IS: \"1\"\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: \"240.0\"\n",
      "(0018, 1000) Device Serial Number                LO: '166003'\n",
      "(0018, 1020) Software Versions                   LO: 'syngo MR E11'\n",
      "(0018, 1030) Protocol Name                       LO: 'T1w_MPR_vNav'\n",
      "(0018, 1251) Transmit Coil Name                  SH: 'Body'\n",
      "(0018, 1310) Acquisition Matrix                  US: [0, 256, 256, 0]\n",
      "(0018, 1312) In-plane Phase Encoding Direction   CS: 'ROW'\n",
      "(0018, 1314) Flip Angle                          DS: \"8.0\"\n",
      "(0018, 1315) Variable Flip Angle Flag            CS: 'N'\n",
      "(0018, 1316) SAR                                 DS: \"0.03557668599229\"\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: \"0.0\"\n",
      "(0019, 100f) [GradientMode]                      SH: 'Fast'\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: [54.86803865, -151.17331696, 130.23434758]\n",
      "(0019, 1017) [SliceResolution]                   DS: \"1.0\"\n",
      "(0019, 1018) [RealDwellTime]                     IS: \"8200\"\n",
      "(0020, 000d) Study Instance UID                  UI: 1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017\n",
      "(0020, 000e) Series Instance UID                 UI: 1.3.12.2.1107.5.2.43.166003.2019061915174069268094190.0.0.0\n",
      "(0020, 0010) Study ID                            SH: '1'\n",
      "(0020, 0011) Series Number                       IS: \"5\"\n",
      "(0020, 0012) Acquisition Number                  IS: \"1\"\n",
      "(0020, 0013) Instance Number                     IS: \"147\"\n",
      "(0020, 0032) Image Position (Patient)            DS: [54.868038654327, -151.17331695557, 130.23434758186]\n",
      "(0020, 0037) Image Orientation (Patient)         DS: [0, 1, 0, 0, 0, -1]\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: \"54.868038654327\"\n",
      "(0028, 0002) Samples per Pixel                   US: 1\n",
      "(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'\n",
      "(0028, 0010) Rows                                US: 256\n",
      "(0028, 0011) Columns                             US: 256\n",
      "(0028, 0030) Pixel Spacing                       DS: [1, 1]\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: 1435\n",
      "(0028, 1050) Window Center                       DS: \"652.0\"\n",
      "(0028, 1051) Window Width                        DS: \"1367.0\"\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 11156 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 140056 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 00.00'\n",
      "(0051, 100b) [AcquisitionMatrixText]             LO: '256*256'\n",
      "(0051, 100c) [Unknown]                           LO: 'FoV 256*256'\n",
      "(0051, 100d) [Unknown]                           SH: 'SP L54.9'\n",
      "(0051, 100e) [Unknown]                           LO: 'Sag'\n",
      "(0051, 100f) [CoilString]                        LO: 'HEA;HEP'\n",
      "(0051, 1011) [PATModeText]                       LO: 'p2'\n",
      "(0051, 1012) [Unknown]                           SH: 'TP 0'\n",
      "(0051, 1013) [PositivePCSDirections]             SH: '+LPH'\n",
      "(0051, 1016) [Unknown]                           LO: 'p2 M/ND/NORM'\n",
      "(0051, 1017) [Unknown]                           SH: 'SL 1.0'\n",
      "(0051, 1019) [Unknown]                           LO: 'A1/IR/WE'\n",
      "(7fe0, 0010) Pixel Data                          OW: Array of 131072 elements\n"
     ]
    }
   ],
   "source": [
    "print(data_set)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The number of TRs collected equals: 103\n",
      "The timing of the TR was: 4200 ms\n",
      "The timing of the TE was: 89 ms\n",
      "The acquisition matrix was: [140, 0, 0, 140] \n",
      "The flip angle in degrees was: 90\n",
      "The acquistion number was: 24 \n",
      "The name of the protocol was: dMRI_AP_REVL\n",
      "The name of the scan was: dMRI_AP_REVL\n",
      "The In-plane Phase Encoding Direction was: COL\n",
      "The Field of View was: FoV 2160*2160\n",
      "The Slice Time was: [0.0, 2167.50000001, 155.0, 2322.50000001, 310.0, 2477.50000001, 465.0, 2632.50000001, 620.0, 2787.50000001, 774.99999999, 2942.5, 929.99999999, 3097.5, 1084.99999999, 3252.5, 1240.00000002, 3407.5, 1395.00000002, 3562.5, 1550.00000002, 3717.5, 1705.00000002, 3870.0, 1857.50000001, 4024.99999999, 2012.50000001, 0.0, 2167.50000001, 155.0, 2322.50000001, 310.0, 2477.50000001, 465.0, 2632.50000001, 620.0, 2787.50000001, 774.99999999, 2942.5, 929.99999999, 3097.5, 1084.99999999, 3252.5, 1240.00000002, 3407.5, 1395.00000002, 3562.5, 1550.00000002, 3717.5, 1705.00000002, 3870.0, 1857.50000001, 4024.99999999, 2012.50000001, 0.0, 2167.50000001, 155.0, 2322.50000001, 310.0, 2477.50000001, 465.0, 2632.50000001, 620.0, 2787.50000001, 774.99999999, 2942.5, 929.99999999, 3097.5, 1084.99999999, 3252.5, 1240.00000002, 3407.5, 1395.00000002, 3562.5, 1550.00000002, 3717.5, 1705.00000002, 3870.0, 1857.50000001, 4024.99999999, 2012.50000001]\n"
     ]
    }
   ],
   "source": [
    "# Elements we're interested in\n",
    "# Repetition Time\n",
    "# Echo Time\n",
    "# Acquisition Matrix \n",
    "# Flip Angle\n",
    "# Acquisition Number\n",
    "# Protocol Name\n",
    "# Slice times = data_set[0x00191029].value\n",
    "\n",
    "print('The number of TRs collected equals: {0}'.format(len(data_files)))\n",
    "print('The timing of the TR was: {0} ms'.format(data_set.RepetitionTime))\n",
    "print('The timing of the TE was: {0} ms'.format(data_set.EchoTime))\n",
    "print('The acquisition matrix was: {0} '.format(data_set.AcquisitionMatrix))\n",
    "print('The flip angle in degrees was: {0}'.format(data_set.FlipAngle))\n",
    "print('The acquistion number was: {0} '.format(data_set.AcquisitionNumber))\n",
    "print('The name of the protocol was: {0}'.format(data_set.ProtocolName))\n",
    "print('The name of the scan was: {0}'.format(data_set.SeriesDescription))\n",
    "\n",
    "# Why use the following format to access information in the header?\n",
    "print('The In-plane Phase Encoding Direction was:', data_set[int('00181312', 16)].value)\n",
    "print('The Field of View was:', data_set[int('0051100c', 16)].value) \n",
    "#alternative approach for doing hexidecimals--\n",
    "#print(data_set[0x0051100c].value)\n",
    "#print(data_set[0x00190100a].value) \n",
    "\n",
    "print('The Slice Time was: {0}'.format(data_set[0x00191029].value))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 109,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The phase encoding direction was: i\n"
     ]
    }
   ],
   "source": [
    "# How do I find phase encoding direction information?\n",
    "import nibabel.nicom.csareader as csareader\n",
    "\n",
    "\n",
    "rowcol_to_niftidim = {'COL': 'i', 'ROW': 'j'}\n",
    "pedp_to_sign = {0: '-', 1: ''} \n",
    "\n",
    "csa_str = data_set[int('00291010', 16)].value\n",
    "csa_tr = csareader.read(csa_str)\n",
    "pedp = csa_tr['tags']['PhaseEncodingDirectionPositive']['items'][0]\n",
    "ij = rowcol_to_niftidim[data_set[int('00181312', 16)].value]\n",
    "sign = pedp_to_sign[pedp]\n",
    "print('The phase encoding direction was: {}{}'.format(ij, sign)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "# 6-fMRI_DistortionMap_PA -- fmri field map dicoms\n",
    "\n",
    "\n",
    "# directories will have to be specific to your computer\n",
    "base_dir = '/Users/emusser/Documents/GitHub'\n",
    "proj_dir = '/mattfeld_2020/code'\n",
    "subj_dir = '/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/'\n",
    "\n",
    "# with strings I can concatenate them with simple addition lines\n",
    "data_dir = base_dir + proj_dir + subj_dir\n",
    "\n",
    "\n",
    "# Here I use glob to grab the dicom files\n",
    "# Why would I use glob?  What does it give me?\n",
    "data_files = glob(data_dir + '/*')\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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'/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-58-9zmsu.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-3-1hf0pp1.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-33-6vjjwe.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-27-2q8so.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-53-1etxk85.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-49-vha1qf.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-37-jinrml.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-18-vlape0.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-54-45gh5z.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-2-1s21i6i.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-34-1abde70.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-45-1t1gszv.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-6-jcslhn.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-30-13qc16a.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-5-qgsyqo.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-55-1krtinf.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-15-1k01co1.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/6-fMRI_DistortionMap_PA/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-6-40-2yx1qf.dcm']\n"
     ]
    }
   ],
   "source": [
    "print(data_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Here I am using the python dicom reader to read in a dicom header\n",
    "# What should go between the square brackets []\n",
    "data_set = dicom.dcmread(data_files[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dataset.file_meta -------------------------------\n",
      "(0002, 0000) File Meta Information Group Length  UL: 204\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: 1.3.12.2.1107.5.2.43.166003.2019061915241161003513836\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', 'NORM']\n",
      "(0008, 0012) Instance Creation Date              DA: '20190619'\n",
      "(0008, 0013) Instance Creation Time              TM: '152413.677000'\n",
      "(0008, 0016) SOP Class UID                       UI: MR Image Storage\n",
      "(0008, 0018) SOP Instance UID                    UI: 1.3.12.2.1107.5.2.43.166003.2019061915241161003513836\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: '152413.328000'\n",
      "(0008, 0032) Acquisition Time                    TM: '151756.262500'\n",
      "(0008, 0033) Content Time                        TM: '152413.677000'\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: 'T1w_MPR_vNav'\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: 1.3.12.2.1107.5.2.43.166003.2019061915163521984993764\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",
      "   (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",
      "(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: ['GR', 'IR']\n",
      "(0018, 0021) Sequence Variant                    CS: ['SK', 'SP', 'MP']\n",
      "(0018, 0022) Scan Options                        CS: ['IR', 'WE']\n",
      "(0018, 0023) MR Acquisition Type                 CS: '3D'\n",
      "(0018, 0024) Sequence Name                       SH: 'tfl3d1_16ns'\n",
      "(0018, 0025) Angio Flag                          CS: 'N'\n",
      "(0018, 0050) Slice Thickness                     DS: \"1.0\"\n",
      "(0018, 0080) Repetition Time                     DS: \"2500.0\"\n",
      "(0018, 0081) Echo Time                           DS: \"2.9\"\n",
      "(0018, 0082) Inversion Time                      DS: \"1070.0\"\n",
      "(0018, 0083) Number of Averages                  DS: \"1.0\"\n",
      "(0018, 0084) Imaging Frequency                   DS: \"123.249149\"\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, 0089) Number of Phase Encoding Steps      IS: \"255\"\n",
      "(0018, 0091) Echo Train Length                   IS: \"1\"\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: \"240.0\"\n",
      "(0018, 1000) Device Serial Number                LO: '166003'\n",
      "(0018, 1020) Software Versions                   LO: 'syngo MR E11'\n",
      "(0018, 1030) Protocol Name                       LO: 'T1w_MPR_vNav'\n",
      "(0018, 1251) Transmit Coil Name                  SH: 'Body'\n",
      "(0018, 1310) Acquisition Matrix                  US: [0, 256, 256, 0]\n",
      "(0018, 1312) In-plane Phase Encoding Direction   CS: 'ROW'\n",
      "(0018, 1314) Flip Angle                          DS: \"8.0\"\n",
      "(0018, 1315) Variable Flip Angle Flag            CS: 'N'\n",
      "(0018, 1316) SAR                                 DS: \"0.03557668599229\"\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: \"0.0\"\n",
      "(0019, 100f) [GradientMode]                      SH: 'Fast'\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: [54.86803865, -151.17331696, 130.23434758]\n",
      "(0019, 1017) [SliceResolution]                   DS: \"1.0\"\n",
      "(0019, 1018) [RealDwellTime]                     IS: \"8200\"\n",
      "(0020, 000d) Study Instance UID                  UI: 1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017\n",
      "(0020, 000e) Series Instance UID                 UI: 1.3.12.2.1107.5.2.43.166003.2019061915174069268094190.0.0.0\n",
      "(0020, 0010) Study ID                            SH: '1'\n",
      "(0020, 0011) Series Number                       IS: \"5\"\n",
      "(0020, 0012) Acquisition Number                  IS: \"1\"\n",
      "(0020, 0013) Instance Number                     IS: \"147\"\n",
      "(0020, 0032) Image Position (Patient)            DS: [54.868038654327, -151.17331695557, 130.23434758186]\n",
      "(0020, 0037) Image Orientation (Patient)         DS: [0, 1, 0, 0, 0, -1]\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: \"54.868038654327\"\n",
      "(0028, 0002) Samples per Pixel                   US: 1\n",
      "(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'\n",
      "(0028, 0010) Rows                                US: 256\n",
      "(0028, 0011) Columns                             US: 256\n",
      "(0028, 0030) Pixel Spacing                       DS: [1, 1]\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: 1435\n",
      "(0028, 1050) Window Center                       DS: \"652.0\"\n",
      "(0028, 1051) Window Width                        DS: \"1367.0\"\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 11156 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 140056 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 00.00'\n",
      "(0051, 100b) [AcquisitionMatrixText]             LO: '256*256'\n",
      "(0051, 100c) [Unknown]                           LO: 'FoV 256*256'\n",
      "(0051, 100d) [Unknown]                           SH: 'SP L54.9'\n",
      "(0051, 100e) [Unknown]                           LO: 'Sag'\n",
      "(0051, 100f) [CoilString]                        LO: 'HEA;HEP'\n",
      "(0051, 1011) [PATModeText]                       LO: 'p2'\n",
      "(0051, 1012) [Unknown]                           SH: 'TP 0'\n",
      "(0051, 1013) [PositivePCSDirections]             SH: '+LPH'\n",
      "(0051, 1016) [Unknown]                           LO: 'p2 M/ND/NORM'\n",
      "(0051, 1017) [Unknown]                           SH: 'SL 1.0'\n",
      "(0051, 1019) [Unknown]                           LO: 'A1/IR/WE'\n",
      "(7fe0, 0010) Pixel Data                          OW: Array of 131072 elements\n"
     ]
    }
   ],
   "source": [
    "print(data_set)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The number of TRs collected equals: 66\n",
      "The timing of the TR was: 2500 ms\n",
      "The timing of the TE was: 2.9 ms\n",
      "The acquisition matrix was: [0, 256, 256, 0] \n",
      "The flip angle in degrees was: 8\n",
      "The acquistion number was: 1 \n",
      "The name of the protocol was: T1w_MPR_vNav\n",
      "The name of the scan was: T1w_MPR_vNav\n",
      "The In-plane Phase Encoding Direction was: ROW\n",
      "The Field of View was: FoV 256*256\n"
     ]
    }
   ],
   "source": [
    "# Elements we're interested in\n",
    "# Repetition Time\n",
    "# Echo Time\n",
    "# Acquisition Matrix \n",
    "# Flip Angle\n",
    "# Acquisition Number\n",
    "# Protocol Name\n",
    "# Slice times = data_set[0x00191029].value\n",
    "\n",
    "print('The number of TRs collected equals: {0}'.format(len(data_files)))\n",
    "print('The timing of the TR was: {0} ms'.format(data_set.RepetitionTime))\n",
    "print('The timing of the TE was: {0} ms'.format(data_set.EchoTime))\n",
    "print('The acquisition matrix was: {0} '.format(data_set.AcquisitionMatrix))\n",
    "print('The flip angle in degrees was: {0}'.format(data_set.FlipAngle))\n",
    "print('The acquistion number was: {0} '.format(data_set.AcquisitionNumber))\n",
    "print('The name of the protocol was: {0}'.format(data_set.ProtocolName))\n",
    "print('The name of the scan was: {0}'.format(data_set.SeriesDescription))\n",
    "\n",
    "# Why use the following format to access information in the header?\n",
    "print('The In-plane Phase Encoding Direction was:', data_set[int('00181312', 16)].value)\n",
    "print('The Field of View was:', data_set[int('0051100c', 16)].value) \n",
    "#alternative approach for doing hexidecimals--\n",
    "#print(data_set[0x0051100c].value)\n",
    "#slice time info doesn't exist with respect to Number of Images in Mosaic there is no hexidecimal 00191029 in this file or the like...\n",
    "#print(data_set[0x00190100a].value) \n",
    "#print('The Slice Time was: {0}'.format(data_set[0x00191029].value)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 108,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The phase encoding direction was: i\n"
     ]
    }
   ],
   "source": [
    "# How do I find phase encoding direction information?\n",
    "import nibabel.nicom.csareader as csareader\n",
    "\n",
    "\n",
    "rowcol_to_niftidim = {'COL': 'i', 'ROW': 'j'}\n",
    "pedp_to_sign = {0: '-', 1: ''} \n",
    "\n",
    "csa_str = data_set[int('00291010', 16)].value\n",
    "csa_tr = csareader.read(csa_str)\n",
    "pedp = csa_tr['tags']['PhaseEncodingDirectionPositive']['items'][0]\n",
    "ij = rowcol_to_niftidim[data_set[int('00181312', 16)].value]\n",
    "sign = pedp_to_sign[pedp]\n",
    "print('The phase encoding direction was: {}{}'.format(ij, sign)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {},
   "outputs": [],
   "source": [
    "# 7-fMRI_DistortionMap_AP -- fmri field map dicoms opposite phase encode direction\n",
    "\n",
    "\n",
    "# directories will have to be specific to your computer\n",
    "base_dir = '/Users/emusser/Documents/GitHub'\n",
    "proj_dir = '/mattfeld_2020/code'\n",
    "subj_dir = '/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/'\n",
    "\n",
    "# with strings I can concatenate them with simple addition lines\n",
    "data_dir = base_dir + proj_dir + subj_dir\n",
    "\n",
    "\n",
    "# Here I use glob to grab the dicom files\n",
    "# Why would I use glob?  What does it give me?\n",
    "data_files = glob(data_dir + '/*')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-10-1tc8ij0.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-9-6lvn4j.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-4-idhn03.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-65-mxt8yo.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-28-1oa045g.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-46-1enuzwr.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-7-1rfwoyb.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-12-40o5p.dcm', 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'/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-17-1pkqsjs.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/7-fMRI_DistortionMap_AP/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-7-27-vponbz.dcm']\n"
     ]
    }
   ],
   "source": [
    "print(data_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Here I am using the python dicom reader to read in a dicom header\n",
    "# What should go between the square brackets []\n",
    "data_set = dicom.dcmread(data_files[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dataset.file_meta -------------------------------\n",
      "(0002, 0000) File Meta Information Group Length  UL: 204\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: 1.3.12.2.1107.5.2.43.166003.2019061915241161003513836\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', 'NORM']\n",
      "(0008, 0012) Instance Creation Date              DA: '20190619'\n",
      "(0008, 0013) Instance Creation Time              TM: '152413.677000'\n",
      "(0008, 0016) SOP Class UID                       UI: MR Image Storage\n",
      "(0008, 0018) SOP Instance UID                    UI: 1.3.12.2.1107.5.2.43.166003.2019061915241161003513836\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: '152413.328000'\n",
      "(0008, 0032) Acquisition Time                    TM: '151756.262500'\n",
      "(0008, 0033) Content Time                        TM: '152413.677000'\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: 'T1w_MPR_vNav'\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: 1.3.12.2.1107.5.2.43.166003.2019061915163521984993764\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",
      "   (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",
      "(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: ['GR', 'IR']\n",
      "(0018, 0021) Sequence Variant                    CS: ['SK', 'SP', 'MP']\n",
      "(0018, 0022) Scan Options                        CS: ['IR', 'WE']\n",
      "(0018, 0023) MR Acquisition Type                 CS: '3D'\n",
      "(0018, 0024) Sequence Name                       SH: 'tfl3d1_16ns'\n",
      "(0018, 0025) Angio Flag                          CS: 'N'\n",
      "(0018, 0050) Slice Thickness                     DS: \"1.0\"\n",
      "(0018, 0080) Repetition Time                     DS: \"2500.0\"\n",
      "(0018, 0081) Echo Time                           DS: \"2.9\"\n",
      "(0018, 0082) Inversion Time                      DS: \"1070.0\"\n",
      "(0018, 0083) Number of Averages                  DS: \"1.0\"\n",
      "(0018, 0084) Imaging Frequency                   DS: \"123.249149\"\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, 0089) Number of Phase Encoding Steps      IS: \"255\"\n",
      "(0018, 0091) Echo Train Length                   IS: \"1\"\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: \"240.0\"\n",
      "(0018, 1000) Device Serial Number                LO: '166003'\n",
      "(0018, 1020) Software Versions                   LO: 'syngo MR E11'\n",
      "(0018, 1030) Protocol Name                       LO: 'T1w_MPR_vNav'\n",
      "(0018, 1251) Transmit Coil Name                  SH: 'Body'\n",
      "(0018, 1310) Acquisition Matrix                  US: [0, 256, 256, 0]\n",
      "(0018, 1312) In-plane Phase Encoding Direction   CS: 'ROW'\n",
      "(0018, 1314) Flip Angle                          DS: \"8.0\"\n",
      "(0018, 1315) Variable Flip Angle Flag            CS: 'N'\n",
      "(0018, 1316) SAR                                 DS: \"0.03557668599229\"\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: \"0.0\"\n",
      "(0019, 100f) [GradientMode]                      SH: 'Fast'\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: [54.86803865, -151.17331696, 130.23434758]\n",
      "(0019, 1017) [SliceResolution]                   DS: \"1.0\"\n",
      "(0019, 1018) [RealDwellTime]                     IS: \"8200\"\n",
      "(0020, 000d) Study Instance UID                  UI: 1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017\n",
      "(0020, 000e) Series Instance UID                 UI: 1.3.12.2.1107.5.2.43.166003.2019061915174069268094190.0.0.0\n",
      "(0020, 0010) Study ID                            SH: '1'\n",
      "(0020, 0011) Series Number                       IS: \"5\"\n",
      "(0020, 0012) Acquisition Number                  IS: \"1\"\n",
      "(0020, 0013) Instance Number                     IS: \"147\"\n",
      "(0020, 0032) Image Position (Patient)            DS: [54.868038654327, -151.17331695557, 130.23434758186]\n",
      "(0020, 0037) Image Orientation (Patient)         DS: [0, 1, 0, 0, 0, -1]\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: \"54.868038654327\"\n",
      "(0028, 0002) Samples per Pixel                   US: 1\n",
      "(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'\n",
      "(0028, 0010) Rows                                US: 256\n",
      "(0028, 0011) Columns                             US: 256\n",
      "(0028, 0030) Pixel Spacing                       DS: [1, 1]\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: 1435\n",
      "(0028, 1050) Window Center                       DS: \"652.0\"\n",
      "(0028, 1051) Window Width                        DS: \"1367.0\"\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 11156 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 140056 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 00.00'\n",
      "(0051, 100b) [AcquisitionMatrixText]             LO: '256*256'\n",
      "(0051, 100c) [Unknown]                           LO: 'FoV 256*256'\n",
      "(0051, 100d) [Unknown]                           SH: 'SP L54.9'\n",
      "(0051, 100e) [Unknown]                           LO: 'Sag'\n",
      "(0051, 100f) [CoilString]                        LO: 'HEA;HEP'\n",
      "(0051, 1011) [PATModeText]                       LO: 'p2'\n",
      "(0051, 1012) [Unknown]                           SH: 'TP 0'\n",
      "(0051, 1013) [PositivePCSDirections]             SH: '+LPH'\n",
      "(0051, 1016) [Unknown]                           LO: 'p2 M/ND/NORM'\n",
      "(0051, 1017) [Unknown]                           SH: 'SL 1.0'\n",
      "(0051, 1019) [Unknown]                           LO: 'A1/IR/WE'\n",
      "(7fe0, 0010) Pixel Data                          OW: Array of 131072 elements\n"
     ]
    }
   ],
   "source": [
    "print(data_set)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The number of TRs collected equals: 66\n",
      "The timing of the TR was: 2500 ms\n",
      "The timing of the TE was: 2.9 ms\n",
      "The acquisition matrix was: [0, 256, 256, 0] \n",
      "The flip angle in degrees was: 8\n",
      "The acquistion number was: 1 \n",
      "The name of the protocol was: T1w_MPR_vNav\n",
      "The name of the scan was: T1w_MPR_vNav\n",
      "The In-plane Phase Encoding Direction was: ROW\n",
      "The Field of View was: FoV 256*256\n"
     ]
    }
   ],
   "source": [
    "# Elements we're interested in\n",
    "# Repetition Time\n",
    "# Echo Time\n",
    "# Acquisition Matrix \n",
    "# Flip Angle\n",
    "# Acquisition Number\n",
    "# Protocol Name\n",
    "# Slice times = data_set[0x00191029].value\n",
    "\n",
    "print('The number of TRs collected equals: {0}'.format(len(data_files)))\n",
    "print('The timing of the TR was: {0} ms'.format(data_set.RepetitionTime))\n",
    "print('The timing of the TE was: {0} ms'.format(data_set.EchoTime))\n",
    "print('The acquisition matrix was: {0} '.format(data_set.AcquisitionMatrix))\n",
    "print('The flip angle in degrees was: {0}'.format(data_set.FlipAngle))\n",
    "print('The acquistion number was: {0} '.format(data_set.AcquisitionNumber))\n",
    "print('The name of the protocol was: {0}'.format(data_set.ProtocolName))\n",
    "print('The name of the scan was: {0}'.format(data_set.SeriesDescription))\n",
    "\n",
    "# Why use the following format to access information in the header?\n",
    "print('The In-plane Phase Encoding Direction was:', data_set[int('00181312', 16)].value)\n",
    "print('The Field of View was:', data_set[int('0051100c', 16)].value) \n",
    "#alternative approach for doing hexidecimals--\n",
    "#print(data_set[0x0051100c].value)\n",
    "#slice time info doesn't exist with respect to Number of Images in Mosaic there is no hexidecimal 00191029 in this file or the like...\n",
    "#print(data_set[0x00190100a].value) \n",
    "#print('The Slice Time was: {0}'.format(data_set[0x00191029].value)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 107,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The phase encoding direction was: i\n"
     ]
    }
   ],
   "source": [
    "# How do I find phase encoding direction information?\n",
    "import nibabel.nicom.csareader as csareader\n",
    "\n",
    "\n",
    "rowcol_to_niftidim = {'COL': 'i', 'ROW': 'j'}\n",
    "pedp_to_sign = {0: '-', 1: ''} \n",
    "\n",
    "csa_str = data_set[int('00291010', 16)].value\n",
    "csa_tr = csareader.read(csa_str)\n",
    "pedp = csa_tr['tags']['PhaseEncodingDirectionPositive']['items'][0]\n",
    "ij = rowcol_to_niftidim[data_set[int('00181312', 16)].value]\n",
    "sign = pedp_to_sign[pedp]\n",
    "print('The phase encoding direction was: {}{}'.format(ij, sign)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "# 9-fMRI_REVL_ROI_loc_2 -- fmri localizer dicoms run1\n",
    "\n",
    "# directories will have to be specific to your computer\n",
    "base_dir = '/Users/emusser/Documents/GitHub'\n",
    "proj_dir = '/mattfeld_2020/code'\n",
    "subj_dir = '/Mattfeld_REVL-000-vCAT-021-S1/scans/9-fMRI_REVL_ROI_loc_2/resources/DICOM/files/'\n",
    "\n",
    "# with strings I can concatenate them with simple addition lines\n",
    "data_dir = base_dir + proj_dir + subj_dir\n",
    "\n",
    "\n",
    "# Here I use glob to grab the dicom files\n",
    "# Why would I use glob?  What does it give me?\n",
    "data_files = glob(data_dir + '/*')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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'/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/9-fMRI_REVL_ROI_loc_2/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-9-106-1j8dule.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/9-fMRI_REVL_ROI_loc_2/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-9-293-au0e9m.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/9-fMRI_REVL_ROI_loc_2/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-9-192-82t0f9.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/9-fMRI_REVL_ROI_loc_2/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-9-95-157956a.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/9-fMRI_REVL_ROI_loc_2/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-9-269-156yzd1.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/9-fMRI_REVL_ROI_loc_2/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-9-129-1a49lvd.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/9-fMRI_REVL_ROI_loc_2/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-9-157-lxo768.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/9-fMRI_REVL_ROI_loc_2/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-9-224-11q4gp6.dcm']\n"
     ]
    }
   ],
   "source": [
    "print(data_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 105,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Here I am using the python dicom reader to read in a dicom header\n",
    "# What should go between the square brackets []\n",
    "data_set = dicom.dcmread(data_files[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dataset.file_meta -------------------------------\n",
      "(0002, 0000) File Meta Information Group Length  UL: 204\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: 1.3.12.2.1107.5.2.43.166003.2019061915241161003513836\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', 'NORM']\n",
      "(0008, 0012) Instance Creation Date              DA: '20190619'\n",
      "(0008, 0013) Instance Creation Time              TM: '152413.677000'\n",
      "(0008, 0016) SOP Class UID                       UI: MR Image Storage\n",
      "(0008, 0018) SOP Instance UID                    UI: 1.3.12.2.1107.5.2.43.166003.2019061915241161003513836\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: '152413.328000'\n",
      "(0008, 0032) Acquisition Time                    TM: '151756.262500'\n",
      "(0008, 0033) Content Time                        TM: '152413.677000'\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: 'T1w_MPR_vNav'\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: 1.3.12.2.1107.5.2.43.166003.2019061915163521984993764\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",
      "   (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",
      "(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: ['GR', 'IR']\n",
      "(0018, 0021) Sequence Variant                    CS: ['SK', 'SP', 'MP']\n",
      "(0018, 0022) Scan Options                        CS: ['IR', 'WE']\n",
      "(0018, 0023) MR Acquisition Type                 CS: '3D'\n",
      "(0018, 0024) Sequence Name                       SH: 'tfl3d1_16ns'\n",
      "(0018, 0025) Angio Flag                          CS: 'N'\n",
      "(0018, 0050) Slice Thickness                     DS: \"1.0\"\n",
      "(0018, 0080) Repetition Time                     DS: \"2500.0\"\n",
      "(0018, 0081) Echo Time                           DS: \"2.9\"\n",
      "(0018, 0082) Inversion Time                      DS: \"1070.0\"\n",
      "(0018, 0083) Number of Averages                  DS: \"1.0\"\n",
      "(0018, 0084) Imaging Frequency                   DS: \"123.249149\"\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, 0089) Number of Phase Encoding Steps      IS: \"255\"\n",
      "(0018, 0091) Echo Train Length                   IS: \"1\"\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: \"240.0\"\n",
      "(0018, 1000) Device Serial Number                LO: '166003'\n",
      "(0018, 1020) Software Versions                   LO: 'syngo MR E11'\n",
      "(0018, 1030) Protocol Name                       LO: 'T1w_MPR_vNav'\n",
      "(0018, 1251) Transmit Coil Name                  SH: 'Body'\n",
      "(0018, 1310) Acquisition Matrix                  US: [0, 256, 256, 0]\n",
      "(0018, 1312) In-plane Phase Encoding Direction   CS: 'ROW'\n",
      "(0018, 1314) Flip Angle                          DS: \"8.0\"\n",
      "(0018, 1315) Variable Flip Angle Flag            CS: 'N'\n",
      "(0018, 1316) SAR                                 DS: \"0.03557668599229\"\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: \"0.0\"\n",
      "(0019, 100f) [GradientMode]                      SH: 'Fast'\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: [54.86803865, -151.17331696, 130.23434758]\n",
      "(0019, 1017) [SliceResolution]                   DS: \"1.0\"\n",
      "(0019, 1018) [RealDwellTime]                     IS: \"8200\"\n",
      "(0020, 000d) Study Instance UID                  UI: 1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017\n",
      "(0020, 000e) Series Instance UID                 UI: 1.3.12.2.1107.5.2.43.166003.2019061915174069268094190.0.0.0\n",
      "(0020, 0010) Study ID                            SH: '1'\n",
      "(0020, 0011) Series Number                       IS: \"5\"\n",
      "(0020, 0012) Acquisition Number                  IS: \"1\"\n",
      "(0020, 0013) Instance Number                     IS: \"147\"\n",
      "(0020, 0032) Image Position (Patient)            DS: [54.868038654327, -151.17331695557, 130.23434758186]\n",
      "(0020, 0037) Image Orientation (Patient)         DS: [0, 1, 0, 0, 0, -1]\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: \"54.868038654327\"\n",
      "(0028, 0002) Samples per Pixel                   US: 1\n",
      "(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'\n",
      "(0028, 0010) Rows                                US: 256\n",
      "(0028, 0011) Columns                             US: 256\n",
      "(0028, 0030) Pixel Spacing                       DS: [1, 1]\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: 1435\n",
      "(0028, 1050) Window Center                       DS: \"652.0\"\n",
      "(0028, 1051) Window Width                        DS: \"1367.0\"\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 11156 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 140056 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 00.00'\n",
      "(0051, 100b) [AcquisitionMatrixText]             LO: '256*256'\n",
      "(0051, 100c) [Unknown]                           LO: 'FoV 256*256'\n",
      "(0051, 100d) [Unknown]                           SH: 'SP L54.9'\n",
      "(0051, 100e) [Unknown]                           LO: 'Sag'\n",
      "(0051, 100f) [CoilString]                        LO: 'HEA;HEP'\n",
      "(0051, 1011) [PATModeText]                       LO: 'p2'\n",
      "(0051, 1012) [Unknown]                           SH: 'TP 0'\n",
      "(0051, 1013) [PositivePCSDirections]             SH: '+LPH'\n",
      "(0051, 1016) [Unknown]                           LO: 'p2 M/ND/NORM'\n",
      "(0051, 1017) [Unknown]                           SH: 'SL 1.0'\n",
      "(0051, 1019) [Unknown]                           LO: 'A1/IR/WE'\n",
      "(7fe0, 0010) Pixel Data                          OW: Array of 131072 elements\n"
     ]
    }
   ],
   "source": [
    "print(data_set)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The number of TRs collected equals: 304\n",
      "The timing of the TR was: 2500 ms\n",
      "The timing of the TE was: 2.9 ms\n",
      "The acquisition matrix was: [0, 256, 256, 0] \n",
      "The flip angle in degrees was: 8\n",
      "The acquistion number was: 1 \n",
      "The name of the protocol was: T1w_MPR_vNav\n",
      "The name of the scan was: T1w_MPR_vNav\n",
      "The In-plane Phase Encoding Direction was: ROW\n",
      "The Field of View was: FoV 256*256\n"
     ]
    }
   ],
   "source": [
    "# Elements we're interested in\n",
    "# Repetition Time\n",
    "# Echo Time\n",
    "# Acquisition Matrix \n",
    "# Flip Angle\n",
    "# Acquisition Number\n",
    "# Protocol Name\n",
    "# Slice times = data_set[0x00191029].value\n",
    "\n",
    "print('The number of TRs collected equals: {0}'.format(len(data_files)))\n",
    "print('The timing of the TR was: {0} ms'.format(data_set.RepetitionTime))\n",
    "print('The timing of the TE was: {0} ms'.format(data_set.EchoTime))\n",
    "print('The acquisition matrix was: {0} '.format(data_set.AcquisitionMatrix))\n",
    "print('The flip angle in degrees was: {0}'.format(data_set.FlipAngle))\n",
    "print('The acquistion number was: {0} '.format(data_set.AcquisitionNumber))\n",
    "print('The name of the protocol was: {0}'.format(data_set.ProtocolName))\n",
    "print('The name of the scan was: {0}'.format(data_set.SeriesDescription))\n",
    "\n",
    "# Why use the following format to access information in the header?\n",
    "print('The In-plane Phase Encoding Direction was:', data_set[int('00181312', 16)].value)\n",
    "print('The Field of View was:', data_set[int('0051100c', 16)].value) \n",
    "#alternative approach for doing hexidecimals--print(data_set[0x0051100c].value)\n",
    "#slice time info doesn't exist with respect to Number of Images in Mosaic there is no hexidecimal 00191029 in this file or the like...print(data_set[0x00190100a].value) \n",
    "#print('The Slice Time was: {0}'.format(data_set[0x00191029].value)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 106,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The phase encoding direction was: i\n"
     ]
    }
   ],
   "source": [
    "# How do I find phase encoding direction information?\n",
    "import nibabel.nicom.csareader as csareader\n",
    "\n",
    "\n",
    "rowcol_to_niftidim = {'COL': 'i', 'ROW': 'j'}\n",
    "pedp_to_sign = {0: '-', 1: ''} \n",
    "\n",
    "csa_str = data_set[int('00291010', 16)].value\n",
    "csa_tr = csareader.read(csa_str)\n",
    "pedp = csa_tr['tags']['PhaseEncodingDirectionPositive']['items'][0]\n",
    "ij = rowcol_to_niftidim[data_set[int('00181312', 16)].value]\n",
    "sign = pedp_to_sign[pedp]\n",
    "print('The phase encoding direction was: {}{}'.format(ij, sign)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# 10-fMRI_REVL_Study_1 -- fmri task dicoms run1\n",
    "# directories will have to be specific to your computer\n",
    "base_dir = '/Users/emusser/Documents/GitHub'\n",
    "proj_dir = '/mattfeld_2020/code'\n",
    "subj_dir = '/Mattfeld_REVL-000-vCAT-021-S1/scans/10-fMRI_REVL_Study_1/resources/DICOM/files/'\n",
    "\n",
    "# with strings I can concatenate them with simple addition lines\n",
    "data_dir = base_dir + proj_dir + subj_dir\n",
    "\n",
    "\n",
    "# Here I use glob to grab the dicom files\n",
    "# Why would I use glob?  What does it give me?\n",
    "data_files = glob(data_dir + '/*')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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'/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/10-fMRI_REVL_Study_1/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-10-141-1oixsej.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/10-fMRI_REVL_Study_1/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-10-98-1tplabe.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/10-fMRI_REVL_Study_1/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-10-122-smdi7x.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/10-fMRI_REVL_Study_1/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-10-251-g86nps.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/10-fMRI_REVL_Study_1/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-10-45-grzneb.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/10-fMRI_REVL_Study_1/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-10-232-2nfpbt.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/10-fMRI_REVL_Study_1/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-10-302-dc5rdn.dcm']\n"
     ]
    }
   ],
   "source": [
    "print(data_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Here I am using the python dicom reader to read in a dicom header\n",
    "# What should go between the square brackets []\n",
    "data_set = dicom.dcmread(data_files[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dataset.file_meta -------------------------------\n",
      "(0002, 0000) File Meta Information Group Length  UL: 204\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: 1.3.12.2.1107.5.2.43.166003.2019061915480017886637273\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', 'MOSAIC']\n",
      "(0008, 0012) Instance Creation Date              DA: '20190619'\n",
      "(0008, 0013) Instance Creation Time              TM: '154835.406000'\n",
      "(0008, 0016) SOP Class UID                       UI: MR Image Storage\n",
      "(0008, 0018) SOP Instance UID                    UI: 1.3.12.2.1107.5.2.43.166003.2019061915480017886637273\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: '154835.373000'\n",
      "(0008, 0032) Acquisition Time                    TM: '154758.855000'\n",
      "(0008, 0033) Content Time                        TM: '154835.406000'\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_REVL_Study_1'\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: 1.3.12.2.1107.5.2.43.166003.2019061915163521984993764\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",
      "(0008, 2112)  Source Image Sequence   66 item(s) ---- \n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475978696737076\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475980084437079\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475982326337084\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475982748237087\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475983123537090\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475983665437093\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475984045737096\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475984494237099\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475984931437102\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475985325037103\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475986843337106\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475988925537109\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475989382037114\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475989789937117\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475990173037119\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475990606137123\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475991008637124\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475991806737127\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475992278037132\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475992661937133\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475993066337136\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475993524137139\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475994002237142\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475994586337145\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475995060637148\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475995667937151\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475996954737156\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475997350637159\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475997775837162\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475998229437165\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475998514037166\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475999147237171\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475999383237172\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915475999903837175\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.20190619154800372437178\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.20190619154800826037183\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548001226137184\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548001692537187\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548002204437190\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548002849137193\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548003444337196\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548004052137199\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548004664237202\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548005327437205\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548005806137208\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548006362337211\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548007010237214\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548007750737217\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548008195137220\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548008716137224\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548009172337227\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191548009617837230\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480010154437233\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480010818137236\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480011337937239\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480011998437242\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480012603537245\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480013187037248\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480013665037251\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480014205237254\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480014823537257\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480015459337260\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480015996837263\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480016401237266\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480016976337269\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061915480017522037272\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'\n",
      "(0018, 0022) Scan Options                        CS: 'FS'\n",
      "(0018, 0023) MR Acquisition Type                 CS: '2D'\n",
      "(0018, 0024) Sequence Name                       SH: 'epfid2d1_90'\n",
      "(0018, 0025) Angio Flag                          CS: 'N'\n",
      "(0018, 0050) Slice Thickness                     DS: \"2.0\"\n",
      "(0018, 0080) Repetition Time                     DS: \"1760.0\"\n",
      "(0018, 0081) Echo Time                           DS: \"35.0\"\n",
      "(0018, 0083) Number of Averages                  DS: \"1.0\"\n",
      "(0018, 0084) Imaging Frequency                   DS: \"123.249153\"\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: \"2.0000000381972\"\n",
      "(0018, 0089) Number of Phase Encoding Steps      IS: \"90\"\n",
      "(0018, 0091) Echo Train Length                   IS: \"90\"\n",
      "(0018, 0093) Percent Sampling                    DS: \"90.0\"\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_REVL_Study_1'\n",
      "(0018, 1251) Transmit Coil Name                  SH: 'Body'\n",
      "(0018, 1310) Acquisition Matrix                  US: [100, 0, 0, 90]\n",
      "(0018, 1312) In-plane Phase Encoding Direction   CS: 'COL'\n",
      "(0018, 1314) Flip Angle                          DS: \"52.0\"\n",
      "(0018, 1315) Variable Flip Angle Flag            CS: 'N'\n",
      "(0018, 1316) SAR                                 DS: \"0.04013631633872\"\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, 100a) [NumberOfImagesInMosaic]            US: 66\n",
      "(0019, 100b) [SliceMeasurementDuration]          DS: \"630000.0\"\n",
      "(0019, 100f) [GradientMode]                      SH: 'Fast*'\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: [-901.7710135, -821.05534252, 406.27493547]\n",
      "(0019, 1016) [TimeAfterStart]                    DS: \"15.315\"\n",
      "(0019, 1017) [SliceResolution]                   DS: \"1.0\"\n",
      "(0019, 1018) [RealDwellTime]                     IS: \"1800\"\n",
      "(0019, 1028) [BandwidthPerPixelPhaseEncode]      FD: 16.393\n",
      "(0019, 1029) [MosaicRefAcqTimes]                 FD: Array of 66 elements\n",
      "(0020, 000d) Study Instance UID                  UI: 1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017\n",
      "(0020, 000e) Series Instance UID                 UI: 1.3.12.2.1107.5.2.43.166003.2019061915471170406436072.0.0.0\n",
      "(0020, 0010) Study ID                            SH: '1'\n",
      "(0020, 0011) Series Number                       IS: \"10\"\n",
      "(0020, 0012) Acquisition Number                  IS: \"6\"\n",
      "(0020, 0013) Instance Number                     IS: \"6\"\n",
      "(0020, 0032) Image Position (Patient)            DS: [-901.77101349831, -821.0553425197, 406.27493547262]\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: \"-58.683259282487\"\n",
      "(0028, 0002) Samples per Pixel                   US: 1\n",
      "(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'\n",
      "(0028, 0010) Rows                                US: 900\n",
      "(0028, 0011) Columns                             US: 900\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: 1350\n",
      "(0028, 1050) Window Center                       DS: \"374.0\"\n",
      "(0028, 1051) Window Width                        DS: \"814.0\"\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 13572 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 147536 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 10:30'\n",
      "(0051, 100b) [AcquisitionMatrixText]             LO: '90*100'\n",
      "(0051, 100c) [Unknown]                           LO: 'FoV 1800*1800'\n",
      "(0051, 100e) [Unknown]                           LO: 'Tra>Cor(-30.0)'\n",
      "(0051, 100f) [CoilString]                        LO: 'HEA;HEP'\n",
      "(0051, 1011) [PATModeText]                       LO: 's3'\n",
      "(0051, 1012) [Unknown]                           SH: 'TP 0'\n",
      "(0051, 1013) [PositivePCSDirections]             SH: '+LPH'\n",
      "(0051, 1016) [Unknown]                           LO: 's3 M/ND/MOSAIC'\n",
      "(0051, 1017) [Unknown]                           SH: 'SL 2.0'\n",
      "(0051, 1019) [Unknown]                           LO: 'A1/FS'\n",
      "(7fe0, 0010) Pixel Data                          OW: Array of 1620000 elements\n"
     ]
    }
   ],
   "source": [
    "print(data_set)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The number of TRs collected equals: 103\n",
      "The timing of the TR was: 4200 ms\n",
      "The timing of the TE was: 89 ms\n",
      "The acquisition matrix was: [140, 0, 0, 140] \n",
      "The flip angle in degrees was: 90\n",
      "The acquistion number was: 24 \n",
      "The name of the protocol was: dMRI_AP_REVL\n",
      "The name of the scan was: dMRI_AP_REVL\n",
      "The In-plane Phase Encoding Direction was: COL\n",
      "The Field of View was: FoV 2160*2160\n",
      "The Slice Time was: [0.0, 2167.50000001, 155.0, 2322.50000001, 310.0, 2477.50000001, 465.0, 2632.50000001, 620.0, 2787.50000001, 774.99999999, 2942.5, 929.99999999, 3097.5, 1084.99999999, 3252.5, 1240.00000002, 3407.5, 1395.00000002, 3562.5, 1550.00000002, 3717.5, 1705.00000002, 3870.0, 1857.50000001, 4024.99999999, 2012.50000001, 0.0, 2167.50000001, 155.0, 2322.50000001, 310.0, 2477.50000001, 465.0, 2632.50000001, 620.0, 2787.50000001, 774.99999999, 2942.5, 929.99999999, 3097.5, 1084.99999999, 3252.5, 1240.00000002, 3407.5, 1395.00000002, 3562.5, 1550.00000002, 3717.5, 1705.00000002, 3870.0, 1857.50000001, 4024.99999999, 2012.50000001, 0.0, 2167.50000001, 155.0, 2322.50000001, 310.0, 2477.50000001, 465.0, 2632.50000001, 620.0, 2787.50000001, 774.99999999, 2942.5, 929.99999999, 3097.5, 1084.99999999, 3252.5, 1240.00000002, 3407.5, 1395.00000002, 3562.5, 1550.00000002, 3717.5, 1705.00000002, 3870.0, 1857.50000001, 4024.99999999, 2012.50000001]\n"
     ]
    }
   ],
   "source": [
    "# Elements we're interested in\n",
    "# Repetition Time\n",
    "# Echo Time\n",
    "# Acquisition Matrix \n",
    "# Flip Angle\n",
    "# Acquisition Number\n",
    "# Protocol Name\n",
    "# Slice times = data_set[0x00191029].value\n",
    "\n",
    "print('The number of TRs collected equals: {0}'.format(len(data_files)))\n",
    "print('The timing of the TR was: {0} ms'.format(data_set.RepetitionTime))\n",
    "print('The timing of the TE was: {0} ms'.format(data_set.EchoTime))\n",
    "print('The acquisition matrix was: {0} '.format(data_set.AcquisitionMatrix))\n",
    "print('The flip angle in degrees was: {0}'.format(data_set.FlipAngle))\n",
    "print('The acquistion number was: {0} '.format(data_set.AcquisitionNumber))\n",
    "print('The name of the protocol was: {0}'.format(data_set.ProtocolName))\n",
    "print('The name of the scan was: {0}'.format(data_set.SeriesDescription))\n",
    "\n",
    "# Why use the following format to access information in the header?\n",
    "print('The In-plane Phase Encoding Direction was:', data_set[int('00181312', 16)].value)\n",
    "print('The Field of View was:', data_set[int('0051100c', 16)].value) \n",
    "#alternative approach for doing hexidecimals--\n",
    "#print(data_set[0x0051100c].value)\n",
    "#slice time info doesn't exist with respect to Number of Images in Mosaic there is no hexidecimal 00191029 in this file or the like...\n",
    "\n",
    "print('The Slice Time was: {0}'.format(data_set[0x00191029].value)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 105,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The phase encoding direction was: i\n"
     ]
    }
   ],
   "source": [
    "# How do I find phase encoding direction information?\n",
    "import nibabel.nicom.csareader as csareader\n",
    "\n",
    "\n",
    "rowcol_to_niftidim = {'COL': 'i', 'ROW': 'j'}\n",
    "pedp_to_sign = {0: '-', 1: ''} \n",
    "\n",
    "csa_str = data_set[int('00291010', 16)].value\n",
    "csa_tr = csareader.read(csa_str)\n",
    "pedp = csa_tr['tags']['PhaseEncodingDirectionPositive']['items'][0]\n",
    "ij = rowcol_to_niftidim[data_set[int('00181312', 16)].value]\n",
    "sign = pedp_to_sign[pedp]\n",
    "print('The phase encoding direction was: {}{}'.format(ij, sign)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [],
   "source": [
    "# 14-dMRI_DistortionMap_AP_dMRI_REVL -- dwi field map dicoms\n",
    "\n",
    "\n",
    "# directories will have to be specific to your computer\n",
    "base_dir = '/Users/emusser/Documents/GitHub'\n",
    "proj_dir = '/mattfeld_2020/code'\n",
    "subj_dir = '/Mattfeld_REVL-000-vCAT-021-S1/scans/14-dMRI_DistortionMap_AP_dMRI_REVL/resources/DICOM/files/'\n",
    "\n",
    "# with strings I can concatenate them with simple addition lines\n",
    "data_dir = base_dir + proj_dir + subj_dir\n",
    "\n",
    "\n",
    "# Here I use glob to grab the dicom files\n",
    "# Why would I use glob?  What does it give me?\n",
    "data_files = glob(data_dir + '/*')\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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'/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/14-dMRI_DistortionMap_AP_dMRI_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-14-49-g2bthf.dcm']\n"
     ]
    }
   ],
   "source": [
    "print(data_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 76,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Here I am using the python dicom reader to read in a dicom header\n",
    "# What should go between the square brackets []\n",
    "data_set = dicom.dcmread(data_files[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 77,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dataset.file_meta -------------------------------\n",
      "(0002, 0000) File Meta Information Group Length  UL: 204\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: 1.3.12.2.1107.5.2.43.166003.2019061916314440169621081\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', 'DIFFUSION', 'NONE', 'ND']\n",
      "(0008, 0012) Instance Creation Date              DA: '20190619'\n",
      "(0008, 0013) Instance Creation Time              TM: '163154.802000'\n",
      "(0008, 0016) SOP Class UID                       UI: MR Image Storage\n",
      "(0008, 0018) SOP Instance UID                    UI: 1.3.12.2.1107.5.2.43.166003.2019061916314440169621081\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: '163154.783000'\n",
      "(0008, 0032) Acquisition Time                    TM: '163143.045000'\n",
      "(0008, 0033) Content Time                        TM: '163154.802000'\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: 'dMRI_DistortionMap_AP_dMRI_REVL'\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: 1.3.12.2.1107.5.2.43.166003.2019061915163521984993764\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191524106394213628\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: ['PFP', 'FS']\n",
      "(0018, 0023) MR Acquisition Type                 CS: '2D'\n",
      "(0018, 0024) Sequence Name                       SH: 'ep_b0'\n",
      "(0018, 0025) Angio Flag                          CS: 'N'\n",
      "(0018, 0050) Slice Thickness                     DS: \"1.7000000476837\"\n",
      "(0018, 0080) Repetition Time                     DS: \"12600.0\"\n",
      "(0018, 0081) Echo Time                           DS: \"89.0\"\n",
      "(0018, 0083) Number of Averages                  DS: \"1.0\"\n",
      "(0018, 0084) Imaging Frequency                   DS: \"123.249172\"\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: \"1.7\"\n",
      "(0018, 0089) Number of Phase Encoding Steps      IS: \"105\"\n",
      "(0018, 0091) Echo Train Length                   IS: \"105\"\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: \"1700.0\"\n",
      "(0018, 1000) Device Serial Number                LO: '166003'\n",
      "(0018, 1020) Software Versions                   LO: 'syngo MR E11'\n",
      "(0018, 1030) Protocol Name                       LO: 'dMRI_DistortionMap_AP_dMRI_REVL'\n",
      "(0018, 1251) Transmit Coil Name                  SH: 'Body'\n",
      "(0018, 1310) Acquisition Matrix                  US: [140, 0, 0, 140]\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: \"0.12464067267085\"\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: \"25000.0\"\n",
      "(0019, 100c) [B_value]                           IS: \"0\"\n",
      "(0019, 100d) [DiffusionDirectionality]           CS: 'NONE'\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: [-122.89651847, -132.47941995, -40.39854813]\n",
      "(0019, 1016) [TimeAfterStart]                    DS: \"1.0875\"\n",
      "(0019, 1017) [SliceResolution]                   DS: \"1.0\"\n",
      "(0019, 1018) [RealDwellTime]                     IS: \"2100\"\n",
      "(0019, 1028) [BandwidthPerPixelPhaseEncode]      FD: 10.352\n",
      "(0020, 000d) Study Instance UID                  UI: 1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017\n",
      "(0020, 000e) Series Instance UID                 UI: 1.3.12.2.1107.5.2.43.166003.2019061916312656812520996.0.0.0\n",
      "(0020, 0010) Study ID                            SH: '1'\n",
      "(0020, 0011) Series Number                       IS: \"14\"\n",
      "(0020, 0012) Acquisition Number                  IS: \"1\"\n",
      "(0020, 0013) Instance Number                     IS: \"15\"\n",
      "(0020, 0032) Image Position (Patient)            DS: [-122.89651846886, -132.47941994667, -40.398548126221]\n",
      "(0020, 0037) Image Orientation (Patient)         DS: [1, 0, 0, 0, 1, 0]\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: \"-40.398548126221\"\n",
      "(0028, 0002) Samples per Pixel                   US: 1\n",
      "(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'\n",
      "(0028, 0010) Rows                                US: 140\n",
      "(0028, 0011) Columns                             US: 140\n",
      "(0028, 0030) Pixel Spacing                       DS: [1.7142857313156, 1.7142857313156]\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: 1689\n",
      "(0028, 1050) Window Center                       DS: \"393.0\"\n",
      "(0028, 1051) Window Width                        DS: \"884.0\"\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 11688 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 166604 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 25.00'\n",
      "(0051, 100b) [AcquisitionMatrixText]             LO: '140p*140'\n",
      "(0051, 100c) [Unknown]                           LO: 'FoV 240*240'\n",
      "(0051, 100d) [Unknown]                           SH: 'SP F40.4'\n",
      "(0051, 100e) [Unknown]                           LO: 'Tra'\n",
      "(0051, 100f) [CoilString]                        LO: 'HEA;HEP'\n",
      "(0051, 1012) [Unknown]                           SH: 'TP 0'\n",
      "(0051, 1013) [PositivePCSDirections]             SH: '+LPH'\n",
      "(0051, 1016) [Unknown]                           LO: 'DIFFUSION/NONE/ND'\n",
      "(0051, 1017) [Unknown]                           SH: 'SL 1.7'\n",
      "(0051, 1019) [Unknown]                           LO: 'A1/PFP/FS'\n",
      "(7fe0, 0010) Pixel Data                          OW: Array of 39200 elements\n"
     ]
    }
   ],
   "source": [
    "print(data_set)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The number of TRs collected equals: 81\n",
      "The timing of the TR was: 12600 ms\n",
      "The timing of the TE was: 89 ms\n",
      "The acquisition matrix was: [140, 0, 0, 140] \n",
      "The flip angle in degrees was: 90\n",
      "The acquistion number was: 1 \n",
      "The name of the protocol was: dMRI_DistortionMap_AP_dMRI_REVL\n",
      "The name of the scan was: dMRI_DistortionMap_AP_dMRI_REVL\n",
      "The In-plane Phase Encoding Direction was: COL\n",
      "The Field of View was: FoV 240*240\n"
     ]
    }
   ],
   "source": [
    "# Elements we're interested in\n",
    "# Repetition Time\n",
    "# Echo Time\n",
    "# Acquisition Matrix \n",
    "# Flip Angle\n",
    "# Acquisition Number\n",
    "# Protocol Name\n",
    "# Slice times = data_set[0x00191029].value\n",
    "\n",
    "print('The number of TRs collected equals: {0}'.format(len(data_files)))\n",
    "print('The timing of the TR was: {0} ms'.format(data_set.RepetitionTime))\n",
    "print('The timing of the TE was: {0} ms'.format(data_set.EchoTime))\n",
    "print('The acquisition matrix was: {0} '.format(data_set.AcquisitionMatrix))\n",
    "print('The flip angle in degrees was: {0}'.format(data_set.FlipAngle))\n",
    "print('The acquistion number was: {0} '.format(data_set.AcquisitionNumber))\n",
    "print('The name of the protocol was: {0}'.format(data_set.ProtocolName))\n",
    "print('The name of the scan was: {0}'.format(data_set.SeriesDescription))\n",
    "\n",
    "# Why use the following format to access information in the header?\n",
    "print('The In-plane Phase Encoding Direction was:', data_set[int('00181312', 16)].value)\n",
    "print('The Field of View was:', data_set[int('0051100c', 16)].value) \n",
    "#alternative approach for doing hexidecimals--\n",
    "#print(data_set[0x0051100c].value)\n",
    "#slice time info doesn't exist with respect to Number of Images in Mosaic there is no hexidecimal 00191029 in this file or the like...\n",
    "#print(data_set[0x00190100a].value) \n",
    "#print('The Slice Time was: {0}'.format(data_set[0x00191029].value)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The phase encoding direction was: i\n"
     ]
    }
   ],
   "source": [
    "# How do I find phase encoding direction information?\n",
    "import nibabel.nicom.csareader as csareader\n",
    "\n",
    "\n",
    "rowcol_to_niftidim = {'COL': 'i', 'ROW': 'j'}\n",
    "pedp_to_sign = {0: '-', 1: ''} \n",
    "\n",
    "csa_str = data_set[int('00291010', 16)].value\n",
    "csa_tr = csareader.read(csa_str)\n",
    "pedp = csa_tr['tags']['PhaseEncodingDirectionPositive']['items'][0]\n",
    "ij = rowcol_to_niftidim[data_set[int('00181312', 16)].value]\n",
    "sign = pedp_to_sign[pedp]\n",
    "print('The phase encoding direction was: {}{}'.format(ij, sign)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "# 16-dMRI_AP_REVL -- diffusion weighted dicoms\n",
    "\n",
    "# directories will have to be specific to your computer\n",
    "base_dir = '/Users/emusser/Documents/GitHub'\n",
    "proj_dir = '/mattfeld_2020/code'\n",
    "subj_dir = '/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/'\n",
    "\n",
    "# with strings I can concatenate them with simple addition lines\n",
    "data_dir = base_dir + proj_dir + subj_dir\n",
    "\n",
    "\n",
    "# Here I use glob to grab the dicom files\n",
    "# Why would I use glob?  What does it give me?\n",
    "data_files = glob(data_dir + '/*')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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'/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-34-cpmmdx.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-10-ayrm2z.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-6-cjs4l6.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-29-10rq2gj.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-53-17sbqnm.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-76-u86iyp.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-11-1clsv53.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-87-1be7f25.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-44-mneulc.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-71-my2jai.dcm', '/Users/emusser/Documents/GitHub/mattfeld_2020/code/Mattfeld_REVL-000-vCAT-021-S1/scans/16-dMRI_AP_REVL/resources/DICOM/files/1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017-16-89-uuz0k6.dcm']\n"
     ]
    }
   ],
   "source": [
    "print(data_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Here I am using the python dicom reader to read in a dicom header\n",
    "# What should go between the square brackets []\n",
    "data_set = dicom.dcmread(data_files[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 83,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Dataset.file_meta -------------------------------\n",
      "(0002, 0000) File Meta Information Group Length  UL: 204\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: 1.3.12.2.1107.5.2.43.166003.2019061916344247531431643\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', 'DIFFUSION', 'NONE', 'ND', 'MOSAIC']\n",
      "(0008, 0012) Instance Creation Date              DA: '20190619'\n",
      "(0008, 0013) Instance Creation Time              TM: '163615.376000'\n",
      "(0008, 0016) SOP Class UID                       UI: MR Image Storage\n",
      "(0008, 0018) SOP Instance UID                    UI: 1.3.12.2.1107.5.2.43.166003.2019061916344247531431643\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: '163435.373000'\n",
      "(0008, 0032) Acquisition Time                    TM: '163437.025000'\n",
      "(0008, 0033) Content Time                        TM: '163615.376000'\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: 'dMRI_AP_REVL'\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: 1.3.12.2.1107.5.2.43.166003.2019061915163521984993764\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",
      "(0008, 2112)  Source Image Sequence   81 item(s) ---- \n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344183761731245\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344184738831249\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344185674431252\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344194050631265\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344194986831270\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344196173131277\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344196571531282\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344197352831287\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344198462231292\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344199693731299\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.20190619163442203731304\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.20190619163442933831309\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634422505031318\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634423017331324\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634423349831326\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634423768931331\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634424246531336\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634425740131347\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634425784231348\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634426585931355\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634426797731359\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634427110731361\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634427819031368\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634428331531371\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634429077331376\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634429475731381\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.201906191634429911131386\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344210595031391\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344212589031406\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344212623231407\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344212649631408\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344212676431409\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344213335631414\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344213961931421\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344214753131426\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344215262631431\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344216685331442\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344216718031443\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344216921431446\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344217782231451\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344218271231456\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344219093131461\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344219174031462\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344220070231467\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344221007431472\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344221044231473\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344221754831476\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344222130431479\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344223857631484\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344226505831495\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344228484231506\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344229284231511\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344229837731516\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344231268731529\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344231302631530\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344231462731533\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344232062531538\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344232456331541\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344233060031548\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344233878331555\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344234047131556\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344234523731561\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344235034931566\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344235757931571\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344235989031574\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344236511031577\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344237516731586\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344237715531587\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344238340731592\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344239160031597\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344240218831602\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344240650531607\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344241538631612\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344242700531621\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344242856131622\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344243769831627\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344244487331630\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344245306631633\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344246252431636\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344246828731639\n",
      "   ---------\n",
      "   (0008, 1150) Referenced SOP Class UID            UI: MR Image Storage\n",
      "   (0008, 1155) Referenced SOP Instance UID         UI: 1.3.12.2.1107.5.2.43.166003.2019061916344247500631642\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: ['PFP', 'FS']\n",
      "(0018, 0023) MR Acquisition Type                 CS: '2D'\n",
      "(0018, 0024) Sequence Name                       SH: 'ep_b3000#23'\n",
      "(0018, 0025) Angio Flag                          CS: 'N'\n",
      "(0018, 0050) Slice Thickness                     DS: \"1.7000000476837\"\n",
      "(0018, 0080) Repetition Time                     DS: \"4200.0\"\n",
      "(0018, 0081) Echo Time                           DS: \"89.0\"\n",
      "(0018, 0083) Number of Averages                  DS: \"1.0\"\n",
      "(0018, 0084) Imaging Frequency                   DS: \"123.249172\"\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: \"1.7\"\n",
      "(0018, 0089) Number of Phase Encoding Steps      IS: \"105\"\n",
      "(0018, 0091) Echo Train Length                   IS: \"105\"\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: \"1700.0\"\n",
      "(0018, 1000) Device Serial Number                LO: '166003'\n",
      "(0018, 1020) Software Versions                   LO: 'syngo MR E11'\n",
      "(0018, 1030) Protocol Name                       LO: 'dMRI_AP_REVL'\n",
      "(0018, 1251) Transmit Coil Name                  SH: 'Body'\n",
      "(0018, 1310) Acquisition Matrix                  US: [140, 0, 0, 140]\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: \"0.23810409618705\"\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, 100a) [NumberOfImagesInMosaic]            US: 81\n",
      "(0019, 100b) [SliceMeasurementDuration]          DS: \"449000.0\"\n",
      "(0019, 100c) [B_value]                           IS: \"3000\"\n",
      "(0019, 100d) [DiffusionDirectionality]           CS: 'DIRECTIONAL'\n",
      "(0019, 100e) [DiffusionGradientDirection]        FD: [0.63655597, -0.09850488, -0.76491398]\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: [-1082.89652801, -1092.47942948, -64.19854736]\n",
      "(0019, 1016) [TimeAfterStart]                    DS: \"113.155\"\n",
      "(0019, 1017) [SliceResolution]                   DS: \"1.0\"\n",
      "(0019, 1018) [RealDwellTime]                     IS: \"2100\"\n",
      "(0019, 1027) [B_matrix]                          FD: [1221.0, -189.0, -1467.0, 29.0, 227.0, 1763.0]\n",
      "(0019, 1028) [BandwidthPerPixelPhaseEncode]      FD: 10.352\n",
      "(0019, 1029) [MosaicRefAcqTimes]                 FD: Array of 81 elements\n",
      "(0020, 000d) Study Instance UID                  UI: 1.3.12.2.1107.5.2.43.166003.30000019061912563618000000017\n",
      "(0020, 000e) Series Instance UID                 UI: 1.3.12.2.1107.5.2.43.166003.2019061916322487110321854.0.0.0\n",
      "(0020, 0010) Study ID                            SH: '1'\n",
      "(0020, 0011) Series Number                       IS: \"16\"\n",
      "(0020, 0012) Acquisition Number                  IS: \"24\"\n",
      "(0020, 0013) Instance Number                     IS: \"24\"\n",
      "(0020, 0032) Image Position (Patient)            DS: [-1082.8965280056, -1092.4794294834, -64.198547363281]\n",
      "(0020, 0037) Image Orientation (Patient)         DS: [1, 0, 0, 0, 1, 0]\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: \"-64.198547363281\"\n",
      "(0028, 0002) Samples per Pixel                   US: 1\n",
      "(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'\n",
      "(0028, 0010) Rows                                US: 1260\n",
      "(0028, 0011) Columns                             US: 1260\n",
      "(0028, 0030) Pixel Spacing                       DS: [1.7142857313156, 1.7142857313156]\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: 489\n",
      "(0028, 1050) Window Center                       DS: \"119.0\"\n",
      "(0028, 1051) Window Width                        DS: \"303.0\"\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 15260 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 166896 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 07:29'\n",
      "(0051, 100b) [AcquisitionMatrixText]             LO: '140p*140'\n",
      "(0051, 100c) [Unknown]                           LO: 'FoV 2160*2160'\n",
      "(0051, 100e) [Unknown]                           LO: 'Tra'\n",
      "(0051, 100f) [CoilString]                        LO: 'HEA;HEP'\n",
      "(0051, 1011) [PATModeText]                       LO: 's3'\n",
      "(0051, 1012) [Unknown]                           SH: 'TP 0'\n",
      "(0051, 1013) [PositivePCSDirections]             SH: '+LPH'\n",
      "(0051, 1016) [Unknown]                           LO: 's3 DIFFUSION/NONE/ND/MOSAIC'\n",
      "(0051, 1017) [Unknown]                           SH: 'SL 1.7'\n",
      "(0051, 1019) [Unknown]                           LO: 'A1/PFP/FS'\n",
      "(7fe0, 0010) Pixel Data                          OW: Array of 3175200 elements\n"
     ]
    }
   ],
   "source": [
    "print(data_set)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The number of TRs collected equals: 103\n",
      "The timing of the TR was: 4200 ms\n",
      "The timing of the TE was: 89 ms\n",
      "The acquisition matrix was: [140, 0, 0, 140] \n",
      "The flip angle in degrees was: 90\n",
      "The acquistion number was: 24 \n",
      "The name of the protocol was: dMRI_AP_REVL\n",
      "The name of the scan was: dMRI_AP_REVL\n",
      "The In-plane Phase Encoding Direction was: COL\n",
      "The Field of View was: FoV 2160*2160\n",
      "The Slice Time was: [0.0, 2167.50000001, 155.0, 2322.50000001, 310.0, 2477.50000001, 465.0, 2632.50000001, 620.0, 2787.50000001, 774.99999999, 2942.5, 929.99999999, 3097.5, 1084.99999999, 3252.5, 1240.00000002, 3407.5, 1395.00000002, 3562.5, 1550.00000002, 3717.5, 1705.00000002, 3870.0, 1857.50000001, 4024.99999999, 2012.50000001, 0.0, 2167.50000001, 155.0, 2322.50000001, 310.0, 2477.50000001, 465.0, 2632.50000001, 620.0, 2787.50000001, 774.99999999, 2942.5, 929.99999999, 3097.5, 1084.99999999, 3252.5, 1240.00000002, 3407.5, 1395.00000002, 3562.5, 1550.00000002, 3717.5, 1705.00000002, 3870.0, 1857.50000001, 4024.99999999, 2012.50000001, 0.0, 2167.50000001, 155.0, 2322.50000001, 310.0, 2477.50000001, 465.0, 2632.50000001, 620.0, 2787.50000001, 774.99999999, 2942.5, 929.99999999, 3097.5, 1084.99999999, 3252.5, 1240.00000002, 3407.5, 1395.00000002, 3562.5, 1550.00000002, 3717.5, 1705.00000002, 3870.0, 1857.50000001, 4024.99999999, 2012.50000001]\n"
     ]
    }
   ],
   "source": [
    "# Elements we're interested in\n",
    "# Repetition Time\n",
    "# Echo Time\n",
    "# Acquisition Matrix \n",
    "# Flip Angle\n",
    "# Acquisition Number\n",
    "# Protocol Name\n",
    "# Slice times = data_set[0x00191029].value\n",
    "\n",
    "print('The number of TRs collected equals: {0}'.format(len(data_files)))\n",
    "print('The timing of the TR was: {0} ms'.format(data_set.RepetitionTime))\n",
    "print('The timing of the TE was: {0} ms'.format(data_set.EchoTime))\n",
    "print('The acquisition matrix was: {0} '.format(data_set.AcquisitionMatrix))\n",
    "print('The flip angle in degrees was: {0}'.format(data_set.FlipAngle))\n",
    "print('The acquistion number was: {0} '.format(data_set.AcquisitionNumber))\n",
    "print('The name of the protocol was: {0}'.format(data_set.ProtocolName))\n",
    "print('The name of the scan was: {0}'.format(data_set.SeriesDescription))\n",
    "\n",
    "# Why use the following format to access information in the header?\n",
    "print('The In-plane Phase Encoding Direction was:', data_set[int('00181312', 16)].value)\n",
    "print('The Field of View was:', data_set[int('0051100c', 16)].value) \n",
    "#alternative approach for doing hexidecimals--\n",
    "#print(data_set[0x0051100c].value)\n",
    "#slice time info doesn't exist with respect to Number of Images in Mosaic there is no hexidecimal 00191029 in this file or the like...\n",
    "#print(data_set[0x00190100a].value) \n",
    "print('The Slice Time was: {0}'.format(data_set[0x00191029].value)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The phase encoding direction was: i\n"
     ]
    }
   ],
   "source": [
    "# How do I find phase encoding direction information?\n",
    "import nibabel.nicom.csareader as csareader\n",
    "\n",
    "\n",
    "rowcol_to_niftidim = {'COL': 'i', 'ROW': 'j'}\n",
    "pedp_to_sign = {0: '-', 1: ''} \n",
    "\n",
    "csa_str = data_set[int('00291010', 16)].value\n",
    "csa_tr = csareader.read(csa_str)\n",
    "pedp = csa_tr['tags']['PhaseEncodingDirectionPositive']['items'][0]\n",
    "ij = rowcol_to_niftidim[data_set[int('00181312', 16)].value]\n",
    "sign = pedp_to_sign[pedp]\n",
    "print('The phase encoding direction was: {}{}'.format(ij, sign)) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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