What Save all of the tabular data (age, height, weight, slice met

Example MRI DICOM meta data <div class="snippet-clipboard-content notranslate posi
Addressed for whole-body MRI <a class="issue-link js-issue-link" data-error-text="Fail
Store MRI metadata in a DataFrame during hd5 production about ml4h HOT 2 CLOSED

ndiamant commented on July 22, 2024
Store MRI metadata in a DataFrame during hd5 production
from ml4h.
Comments (2)

mklarqvist commented on July 22, 2024
Example MRI DICOM meta data
Dataset.file_meta -------------------------------
(0002, 0000) File Meta Information Group Length  UL: 214
(0002, 0001) File Meta Information Version       OB: b'\x00\x01'
(0002, 0002) Media Storage SOP Class UID         UI: MR Image Storage
(0002, 0003) Media Storage SOP Instance UID      UI: <HIDDEN>
(0002, 0010) Transfer Syntax UID                 UI: Explicit VR Little Endian
(0002, 0012) Implementation Class UID            UI: <HIDDEN>
(0002, 0013) Implementation Version Name         SH: 'OFFIS_DCMBP_360'
(0002, 0016) Source Application Entity Title     AE: 'AWP141243'
-------------------------------------------------
(0008, 0005) Specific Character Set              CS: 'ISO_IR 100'
(0008, 0008) Image Type                          CS: ['ORIGINAL', 'PRIMARY', 'M', 'DIS2D']
(0008, 0012) Instance Creation Date              DA: '20170718'
(0008, 0013) Instance Creation Time              TM: '094203.128000'
(0008, 0016) SOP Class UID                       UI: MR Image Storage
(0008, 0018) SOP Instance UID                    UI: <HIDDEN>
(0008, 0020) Study Date                          DA: '20170718'
(0008, 0021) Series Date                         DA: '20170718'
(0008, 0022) Acquisition Date                    DA: '20170718'
(0008, 0023) Content Date                        DA: '20170718'
(0008, 0030) Study Time                          TM: <HIDDEN>
(0008, 0031) Series Time                         TM: <HIDDEN>
(0008, 0032) Acquisition Time                    TM: '094136.542500'
(0008, 0033) Content Time                        TM: '094203.128000'
(0008, 0050) Accession Number                    SH: ''
(0008, 0060) Modality                            CS: 'MR'
(0008, 0070) Manufacturer                        LO: 'SIEMENS'
(0008, 0080) Institution Name                    LO: 'UK Biobank'
(0008, 0081) Institution Address                 ST: 'Hawick Trading Estate StreetNo,Newcastle upon Tyne,District,GB,NE6 1AS'
(0008, 0090) Referring Physician's Name          PN: ''
(0008, 1010) Station Name                        SH: 'AWP141243'
(0008, 1030) Study Description                   LO: 'UKBB^abdomen'
(0008, 103e) Series Description                  LO: 'Dixon_noBH_in'
(0008, 1040) Institutional Department Name       LO: 'Department'
(0008, 1050) Performing Physician's Name         PN: ''
(0008, 1090) Manufacturer's Model Name           LO: 'Aera'
(0010, 0010) Patient's Name                      PN: <HIDDEN>
(0010, 0020) Patient ID                          LO: <HIDDEN>
(0010, 0030) Patient's Birth Date                DA: <HIDDEN>
(0010, 0040) Patient's Sex                       CS: <HIDDEN>
(0010, 1010) Patient's Age                       AS: <HIDDEN>
(0010, 1020) Patient's Size                      DS: <HIDDEN>
(0010, 1030) Patient's Weight                    DS: <HIDDEN>
(0018, 0015) Body Part Examined                  CS: 'ABDOMEN'
(0018, 0020) Scanning Sequence                   CS: 'GR'
(0018, 0021) Sequence Variant                    CS: ['SP', 'OSP']
(0018, 0022) Scan Options                        CS: 'PFP'
(0018, 0023) MR Acquisition Type                 CS: '3D'
(0018, 0024) Sequence Name                       SH: '*fl3d2'
(0018, 0025) Angio Flag                          CS: 'N'
(0018, 0050) Slice Thickness                     DS: "3.0"
(0018, 0080) Repetition Time                     DS: "6.67"
(0018, 0081) Echo Time                           DS: "4.77"
(0018, 0083) Number of Averages                  DS: "1.0"
(0018, 0084) Imaging Frequency                   DS: "63.67827"
(0018, 0085) Imaged Nucleus                      SH: '1H'
(0018, 0086) Echo Number(s)                      IS: "2"
(0018, 0087) Magnetic Field Strength             DS: "1.5"
(0018, 0089) Number of Phase Encoding Steps      IS: "90"
(0018, 0091) Echo Train Length                   IS: "2"
(0018, 0093) Percent Sampling                    DS: "71.0"
(0018, 0094) Percent Phase Field of View         DS: "75.0"
(0018, 0095) Pixel Bandwidth                     DS: "440.0"
(0018, 1000) Device Serial Number                LO: '141243'
(0018, 1020) Software Versions                   LO: 'syngo MR D13'
(0018, 1030) Protocol Name                       LO: 'Dixon_noBH'
(0018, 1251) Transmit Coil Name                  SH: 'Body'
(0018, 1310) Acquisition Matrix                  US: [224, 0, 0, 119]
(0018, 1312) In-plane Phase Encoding Direction   CS: 'COL'
(0018, 1314) Flip Angle                          DS: "10.0"
(0018, 1315) Variable Flip Angle Flag            CS: 'N'
(0018, 1316) SAR                                 DS: "0.15825931900621"
(0018, 1318) dB/dt                               DS: "0.0"
(0018, 5100) Patient Position                    CS: 'HFS'
(0019, 0010) Private Creator                     LO: 'SIEMENS MR HEADER'
(0019, 1008) [CSA Image Header Type]             CS: 'IMAGE NUM 4'
(0019, 1009) [CSA Image Header Version ??]       LO: '1.0'
(0019, 100b) [SliceMeasurementDuration]          DS: "23897.5"
(0019, 100f) [GradientMode]                      SH: 'Fast'
(0019, 1011) [FlowCompensation]                  SH: 'No'
(0019, 1012) [TablePositionOrigin]               SL: [0, 0, -1183]
(0019, 1013) [ImaAbsTablePosition]               SL: [0, 0, -1213]
(0019, 1014) [ImaRelTablePosition]               IS: [0, 0, -30]
(0019, 1015) [SlicePosition_PCS]                 FD: [-250.00000763, -187.50000572, -49.5]
(0019, 1017) [SliceResolution]                   DS: "1.0"
(0019, 1018) [RealDwellTime]                     IS: "5100"
(0020, 000d) Study Instance UID                  UI: <HIDDEN>
(0020, 000e) Series Instance UID                 UI: <HIDDEN>
(0020, 0010) Study ID                            SH: '1'
(0020, 0011) Series Number                       IS: "1"
(0020, 0012) Acquisition Number                  IS: "1"
(0020, 0013) Instance Number                     IS: "49"
(0020, 0032) Image Position (Patient)            DS: [-250.00000762939, -187.50000572205, -79.5]
(0020, 0037) Image Orientation (Patient)         DS: [1, 0, 0, 0, 1, 0]
(0020, 0052) Frame of Reference UID              UI: <HIDDEN>
(0020, 1040) Position Reference Indicator        LO: ''
(0020, 1041) Slice Location                      DS: "-79.5"
(0028, 0002) Samples per Pixel                   US: 1
(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'
(0028, 0010) Rows                                US: 168
(0028, 0011) Columns                             US: 224
(0028, 0030) Pixel Spacing                       DS: [2.2321429252625, 2.2321429252625]
(0028, 0100) Bits Allocated                      US: 16
(0028, 0101) Bits Stored                         US: 12
(0028, 0102) High Bit                            US: 11
(0028, 0103) Pixel Representation                US: 0
(0028, 0106) Smallest Image Pixel Value          US: 0
(0028, 0107) Largest Image Pixel Value           US: 1090
(0028, 1050) Window Center                       DS: "657.0"
(0028, 1051) Window Width                        DS: "1342.0"
(0028, 1055) Window Center & Width Explanation   LO: 'Algo1'
(0029, 0010) Private Creator                     LO: 'SIEMENS CSA HEADER'
(0029, 0011) Private Creator                     LO: 'SIEMENS MEDCOM HEADER2'
(0029, 1008) [CSA Image Header Type]             CS: 'IMAGE NUM 4'
(0029, 1009) [CSA Image Header Version]          LO: '20170718'
(0029, 1010) [CSA Image Header Info]             OB: Array of 10848 elements
(0029, 1018) [CSA Series Header Type]            CS: 'MR'
(0029, 1019) [CSA Series Header Version]         LO: '20170718'
(0029, 1020) [CSA Series Header Info]            OB: Array of 79760 elements
(0029, 1160) [Series Workflow Status]            LO: 'com'
(0032, 1060) Requested Procedure Description     LO: 'UKBB abdomen'
(0040, 0244) Performed Procedure Step Start Date DA: '20170718'
(0040, 0245) Performed Procedure Step Start Time TM: '094016.953000'
(0040, 0253) Performed Procedure Step ID         SH: 'MR20170718094016'
(0040, 0254) Performed Procedure Step Descriptio LO: 'UKBB^abdomen'
(0040, 0280) Comments on the Performed Procedure ST: ''
(0051, 0010) Private Creator                     LO: 'SIEMENS MR HEADER'
(0051, 1008) [CSA Image Header Type]             CS: 'IMAGE NUM 4'
(0051, 1009) [CSA Image Header Version ??]       LO: '1.0'
(0051, 100a) [Unknown]                           LO: 'TA 23.89'
(0051, 100b) [AcquisitionMatrixText]             LO: '119p*224'
(0051, 100c) [Unknown]                           LO: 'FoV 375*500'
(0051, 100d) [Unknown]                           SH: 'SP F79.5'
(0051, 100e) [Unknown]                           LO: 'Tra'
(0051, 100f) [CoilString]                        LO: 'BC'
(0051, 1012) [Unknown]                           SH: 'TP F30'
(0051, 1013) [PositivePCSDirections]             SH: '+LPH'
(0051, 1016) [Unknown]                           LO: 'M/DIS2D'
(0051, 1017) [Unknown]                           SH: 'SL 3.0'
(0051, 1019) [Unknown]                           LO: 'A1/PFP'
(7fe0, 0010) Pixel Data                          OW: Array of 75264 elements
from ml4h.
mklarqvist commented on July 22, 2024
Addressed for whole-body MRI #425
from ml4h.
Store MRI metadata in a DataFrame during hd5 production about ml4h HOT 2 CLOSED

Comments (2)

Related Issues (20)

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent
