CT影像文件格式DICOM详解

CT影像文件格式DICOM详解

DICOM简介

DICOM（Digital Imaging and Communications in Medicine）即医学数字成像和通信，是医学图像和相关信息的国际标准（ISO 12052）。DICOM被广泛应用于放射医疗，心血管成像以及放射诊疗诊断设备（X射线，CT，核磁共振，超声等），并且在眼科和牙科等其它医学领域得到越来越深入广泛的应用。所有患者的医学图像都以 DICOM 文件格式进行存储。这个格式包含关于患者的 PHI（protected health information，https://en.wikipedia.org/wiki/Protected_health_information ）信息，例如姓名，性别，年龄，以及其他图像相关信息比如捕获并生成图像的设备信息，医疗的一些上下文相关信息等。医学图像设备生成 DICOM 文件，医生使用 DICOM 阅读器（能够显示 DICOM 图像的计算机软件）阅读并对图像中发现的问题进行诊断。本人推荐的DICOM 阅读器为Mango

目前采用的标准是DICOM3.0，每一张图像中都携带着大量的信息，这些信息具体可以分为以下四类：（a）Patient（b）Study（c）Series（d）Image。每一个DICOM Tag都是由两个十六进制数的组合来确定的，分别为Group和Element。如(0010,0010)这个Tag表示的是Patient’s Name，它存储着这张DICOM图像的患者姓名。

一张CT图像有 512x512 个像素点，在dicom文件中每个像素由2字节表示，所以每张图片约512KB大小。图像中每个像素都是整数，专业名称为 Hounsfield scale 或 CT Number，是描述物质的放射密度的量化值(参考Wikipedia)。下表为常见物质的HU值。

DICOM信息获取
我们暂时不关注dicom信息的具体格式，我们关注如何用python获取到相关的信息以及那些信息是比较重要的。我们能获取到的信息分为两类：1.DICOM文件信息 2.DICOM具体的数据
获取信息的相关代码如下：

import pydicom as dicom

DATA_PATH = 'J:/dataset/LIDC-IDRI/LIDC-IDRI/LIDC-IDRI-0001/01-01-2000-30178/3000566-03192/'

#获取Dicom文件信息说明
f = dicom.read_file(DATA_PATH + '000001.dcm')
print(f)

import SimpleITK as sitk
import cv2
import matplotlib.pyplot as plt

#获取Dicom数据
ds = sitk.ReadImage(DATA_PATH + '000001.dcm')
img_array = sitk.GetArrayFromImage(ds)

print(img_array.shape)
plt.imshow(img_array[0],cmap="gray")
plt.show()

Dicom文件信息显示如下：

(0008, 0005) Specific Character Set              CS: 'ISO_IR 100'
(0008, 0008) Image Type                          CS: ['ORIGINAL', 'PRIMARY', 'AXIAL']
(0008, 0016) SOP Class UID                       UI: CT Image Storage
(0008, 0018) SOP Instance UID                    UI: 1.3.6.1.4.1.14519.5.2.1.6279.6001.143451261327128179989900675595
(0008, 0020) Study Date                          DA: '20000101'
(0008, 0021) Series Date                         DA: '20000101'
(0008, 0022) Acquisition Date                    DA: '20000101'
(0008, 0023) Content Date                        DA: '20000101'
(0008, 0024) Overlay Date                        DA: '20000101'
(0008, 0025) Curve Date                          DA: '20000101'
(0008, 002a) Acquisition DateTime                DT: '20000101'
(0008, 0030) Study Time                          TM: ''
(0008, 0032) Acquisition Time                    TM: ''
(0008, 0033) Content Time                        TM: ''
(0008, 0050) Accession Number                    SH: '2819497684894126'
(0008, 0060) Modality                            CS: 'CT'
(0008, 0070) Manufacturer                        LO: 'GE MEDICAL SYSTEMS'
(0008, 0090) Referring Physician's Name          PN: ''
(0008, 1090) Manufacturer's Model Name           LO: 'LightSpeed Plus'
(0008, 1155) Referenced SOP Instance UID         UI: 1.3.6.1.4.1.14519.5.2.1.6279.6001.675906998158803995297223798692
(0010, 0010) Patient's Name                      PN: ''
(0010, 0020) Patient ID                          LO: 'LIDC-IDRI-0001'
(0010, 0030) Patient's Birth Date                DA: ''
(0010, 0040) Patient's Sex                       CS: ''
(0010, 1010) Patient's Age                       AS: ''
(0010, 21d0) Last Menstrual Date                 DA: '20000101'
(0012, 0062) Patient Identity Removed            CS: 'YES'
(0012, 0063) De-identification Method            LO: 'DCM:113100/113105/113107/113108/113109/113111'
(0013, 0010) Private Creator                     LO: 'CTP'
(0013, 1010) Private tag data                    LO: 'LIDC-IDRI'
(0013, 1013) Private tag data                    LO: '62796001'
(0018, 0010) Contrast/Bolus Agent                LO: 'IV'
(0018, 0015) Body Part Examined                  CS: 'CHEST'
(0018, 0022) Scan Options                        CS: 'HELICAL MODE'
(0018, 0050) Slice Thickness                     DS: "2.500000"
(0018, 0060) KVP                                 DS: "120"
(0018, 0090) Data Collection Diameter            DS: "500.000000"
(0018, 1020) Software Version(s)                 LO: 'LightSpeedApps2.4.2_H2.4M5'
(0018, 1100) Reconstruction Diameter             DS: "360.000000"
(0018, 1110) Distance Source to Detector         DS: "949.075012"
(0018, 1111) Distance Source to Patient          DS: "541.000000"
(0018, 1120) Gantry/Detector Tilt                DS: "0.000000"
(0018, 1130) Table Height                        DS: "144.399994"
(0018, 1140) Rotation Direction                  CS: 'CW'
(0018, 1150) Exposure Time                       IS: "570"
(0018, 1151) X-Ray Tube Current                  IS: "400"
(0018, 1152) Exposure                            IS: "4684"
(0018, 1160) Filter Type                         SH: 'BODY FILTER'
(0018, 1170) Generator Power                     IS: "48000"
(0018, 1190) Focal Spot(s)                       DS: "1.200000"
(0018, 1210) Convolution Kernel                  SH: 'STANDARD'
(0018, 5100) Patient Position                    CS: 'FFS'
(0020, 000d) Study Instance UID                  UI: 1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178
(0020, 000e) Series Instance UID                 UI: 1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192
(0020, 0010) Study ID                            SH: ''
(0020, 0011) Series Number                       IS: "3000566"
(0020, 0013) Instance Number                     IS: "80"
(0020, 0032) Image Position (Patient)            DS: ['-166.000000', '-171.699997', '-207.500000']
(0020, 0037) Image Orientation (Patient)         DS: ['1.000000', '0.000000', '0.000000', '0.000000', '1.000000', '0.000000']
(0020, 0052) Frame of Reference UID              UI: 1.3.6.1.4.1.14519.5.2.1.6279.6001.229925374658226729607867499499
(0020, 1040) Position Reference Indicator        LO: 'SN'
(0020, 1041) Slice Location                      DS: "-207.500000"
(0028, 0002) Samples per Pixel                   US: 1
(0028, 0004) Photometric Interpretation          CS: 'MONOCHROME2'
(0028, 0010) Rows                                US: 512
(0028, 0011) Columns                             US: 512
(0028, 0030) Pixel Spacing                       DS: ['0.703125', '0.703125']
(0028, 0100) Bits Allocated                      US: 16
(0028, 0101) Bits Stored                         US: 16
(0028, 0102) High Bit                            US: 15
(0028, 0103) Pixel Representation                US: 1
(0028, 0120) Pixel Padding Value                 US: 63536
(0028, 0303) Longitudinal Temporal Information M CS: 'MODIFIED'
(0028, 1050) Window Center                       DS: "-600"
(0028, 1051) Window Width                        DS: "1600"
(0028, 1052) Rescale Intercept                   DS: "-1024"
(0028, 1053) Rescale Slope                       DS: "1"
(0038, 0020) Admitting Date                      DA: '20000101'
(0040, 0002) Scheduled Procedure Step Start Date DA: '20000101'
(0040, 0004) Scheduled Procedure Step End Date   DA: '20000101'
(0040, 0244) Performed Procedure Step Start Date DA: '20000101'
(0040, 2016) Placer Order Number / Imaging Servi LO: ''
(0040, 2017) Filler Order Number / Imaging Servi LO: ''
(0040, a075) Verifying Observer Name             PN: 'Removed by CTP'
(0040, a123) Person Name                         PN: 'Removed by CTP'
(0040, a124) UID                                 UI: 1.3.6.1.4.1.14519.5.2.1.6279.6001.335419887712224178340067932923
(0070, 0084) Content Creator's Name              PN: ''
(0088, 0140) Storage Media File-set UID          UI: 1.3.6.1.4.1.14519.5.2.1.6279.6001.211790042620307056609660772296
(7fe0, 0010) Pixel Data                          OW: Array of 524288 elements

DICOM的常用Tag分类和说明

数据显示成灰度图的结果如下：