很高兴在雪易的CSDN遇见你 

VTK技术爱好者 QQ：870202403      公众号：VTK忠粉

---

前言

本文分享开源软件TotalSegmentator，该开源项目针对CT/MRI数据类型，对主要的解剖学结构进行自动分割，并且被集成到MITK中。希望对各位小伙伴有所帮助！

感谢各位小伙伴的点赞+关注，小易会继续努力分享，一起进步！

你的点赞就是我的动力(＾Ｕ＾)ノ~ＹＯ

---

目录

前言

1. TotalSegmentator介绍

2. TotalSegmentator下载&安装

3. TotalSegmentator的使用

3.1 CT/MR数据分割

3.2 子任务

3.4 高级设置

3.3 CT分割类别

3.4 MR分割类别

结论：

---

1. TotalSegmentator介绍

        TotalSegmentator由巴塞尔大学医院研究与分析部门创建，可以针对任何CT或MR数据进行主要解剖结构进行分割。它基于广泛的CT/MRI的训练数据（不同的扫描设备，不同的机构，不同的协议等），因此在大部分数据上都有很好的结果。

CT数据集：

Dataset with segmentations of 117 important anatomical structures in 1228 CT images (zenodo.org)

MR数据集：

Dataset with segmentations of 117 important anatomical structures in 1228 CT images (zenodo.org)

支持的CT分类如下：

 支持的MR分类如下：

2. TotalSegmentator下载&安装

GitHub地址：GitHub - wasserth/TotalSegmentator: Tool for robust segmentation of >100 important anatomical structures in CT and MR images

TotalSegmentator安装依赖于Python & Pytorch

Pytorch的安装教程 

TotalSegmentator安装

        安装命令： pip install TotalSegmentator   

        安装命令： pip install TotalSegmentator==2.1.0

安装成功标志

TotalSegmentator使用了诸多我们熟悉的第三方库，如opencv, simple-itk, vtk 等。 

3. TotalSegmentator的使用

3.1 CT/MR数据分割

TotalSegmentator -i ct.nii.gz -o segmentations

TotalSegmentator -i mri.nii.gz -o segmentations --task total_mr

注意：输入可以时Nifti数据格式，或文件夹或压缩文件，需要包含一个患者的全部DICOM切片。如果在CPU上进行分割，可以使用 --fast 或  --roi_subset 来提高效率。

3.2 子任务

分割时的选项

• total: 默认分割包括117个主类。用于CT数据。
• total_mr: 默认分割包括56个主类，用于MR数据
• lung_vessels: 肺血管，支气管
• body: 身体，躯干，四肢，皮肤
• cerebral_bleed: 颅内出血*
• hip_implant: 髋关节假体*
• coronary_arteries: 冠状动脉*
• pleural_pericard_effusion: 胸腔积液, 心包积液*

注意：带*的表示采用小的数据集进行训练的模型，可能分割效果没那么好。

使用方法：

TotalSegmentator -i ct.nii.gz -o segmentations -ta <task_name>

3.4 高级设置

• --device: Choose cpu or gpu or gpu:X (e.g., gpu:1 -> cuda:1)
• --fast: For faster runtime and less memory requirements use this option. It will run a lower resolution model (3mm instead of 1.5mm).
• --roi_subset: Takes a space-separated list of class names (e.g. spleen colon brain) and only predicts those classes. Saves a lot of runtime and memory. Might be less accurate especially for small classes (e.g. prostate).
• --preview: This will generate a 3D rendering of all classes, giving you a quick overview if the segmentation worked and where it failed (see preview.png in output directory).
• --ml: This will save one nifti file containing all labels instead of one file for each class. Saves runtime during saving of nifti files. (see here for index to class name mapping).
• --statistics: This will generate a file statistics.json with volume (in mm³) and mean intensity of each class.
• --radiomics: This will generate a file statistics_radiomics.json with the radiomics features of each class. You have to install pyradiomics to use this (pip install pyradiomics).

3.3 CT分割类别

Index	TotalSegmentator name	TA2 name
1	spleen
2	kidney_right
3	kidney_left
4	gallbladder
5	liver
6	stomach
7	pancreas
8	adrenal_gland_right	suprarenal gland
9	adrenal_gland_left	suprarenal gland
10	lung_upper_lobe_left	superior lobe of left lung
11	lung_lower_lobe_left	inferior lobe of left lung
12	lung_upper_lobe_right	superior lobe of right lung
13	lung_middle_lobe_right	middle lobe of right lung
14	lung_lower_lobe_right	inferior lobe of right lung
15	esophagus
16	trachea
17	thyroid_gland
18	small_bowel	small intestine
19	duodenum
20	colon
21	urinary_bladder
22	prostate
23	kidney_cyst_left
24	kidney_cyst_right
25	sacrum
26	vertebrae_S1
27	vertebrae_L5
28	vertebrae_L4
29	vertebrae_L3
30	vertebrae_L2
31	vertebrae_L1
32	vertebrae_T12
33	vertebrae_T11
34	vertebrae_T10
35	vertebrae_T9
36	vertebrae_T8
37	vertebrae_T7
38	vertebrae_T6
39	vertebrae_T5
40	vertebrae_T4
41	vertebrae_T3
42	vertebrae_T2
43	vertebrae_T1
44	vertebrae_C7
45	vertebrae_C6
46	vertebrae_C5
47	vertebrae_C4
48	vertebrae_C3
49	vertebrae_C2
50	vertebrae_C1
51	heart
52	aorta
53	pulmonary_vein
54	brachiocephalic_trunk
55	subclavian_artery_right
56	subclavian_artery_left
57	common_carotid_artery_right
58	common_carotid_artery_left
59	brachiocephalic_vein_left
60	brachiocephalic_vein_right
61	atrial_appendage_left
62	superior_vena_cava
63	inferior_vena_cava
64	portal_vein_and_splenic_vein	hepatic portal vein
65	iliac_artery_left	common iliac artery
66	iliac_artery_right	common iliac artery
67	iliac_vena_left	common iliac vein
68	iliac_vena_right	common iliac vein
69	humerus_left
70	humerus_right
71	scapula_left
72	scapula_right
73	clavicula_left	clavicle
74	clavicula_right	clavicle
75	femur_left
76	femur_right
77	hip_left
78	hip_right
79	spinal_cord
80	gluteus_maximus_left	gluteus maximus muscle
81	gluteus_maximus_right	gluteus maximus muscle
82	gluteus_medius_left	gluteus medius muscle
83	gluteus_medius_right	gluteus medius muscle
84	gluteus_minimus_left	gluteus minimus muscle
85	gluteus_minimus_right	gluteus minimus muscle
86	autochthon_left
87	autochthon_right
88	iliopsoas_left	iliopsoas muscle
89	iliopsoas_right	iliopsoas muscle
90	brain
91	skull
92	rib_left_1
93	rib_left_2
94	rib_left_3
95	rib_left_4
96	rib_left_5
97	rib_left_6
98	rib_left_7
99	rib_left_8
100	rib_left_9
101	rib_left_10
102	rib_left_11
103	rib_left_12
104	rib_right_1
105	rib_right_2
106	rib_right_3
107	rib_right_4
108	rib_right_5
109	rib_right_6
110	rib_right_7
111	rib_right_8
112	rib_right_9
113	rib_right_10
114	rib_right_11
115	rib_right_12
116	sternum
117	costal_cartilages

3.4 MR分割类别

Index	TotalSegmentator name	TA2 name
1	spleen
2	kidney_right
3	kidney_left
4	gallbladder
5	liver
6	stomach
7	pancreas
8	adrenal_gland_right	suprarenal gland
9	adrenal_gland_left	suprarenal gland
10	lung_left
11	lung_right
12	esophagus
13	small_bowel	small intestine
14	duodenum
15	colon
16	urinary_bladder
17	prostate
18	sacrum
19	vertebrae
20	intervertebral_discs
21	spinal_cord
22	heart
23	aorta
24	inferior_vena_cava
25	portal_vein_and_splenic_vein	hepatic portal vein
26	iliac_artery_left	common iliac artery
27	iliac_artery_right	common iliac artery
28	iliac_vena_left	common iliac vein
29	iliac_vena_right	common iliac vein
30	humerus_left
31	humerus_right
32	fibula
33	tibia
34	femur_left
35	femur_right
36	hip_left
37	hip_right
38	gluteus_maximus_left	gluteus maximus muscle
39	gluteus_maximus_right	gluteus maximus muscle
40	gluteus_medius_left	gluteus medius muscle
41	gluteus_medius_right	gluteus medius muscle
42	gluteus_minimus_left	gluteus minimus muscle
43	gluteus_minimus_right	gluteus minimus muscle
44	autochthon_left
45	autochthon_right
46	iliopsoas_left	iliopsoas muscle
47	iliopsoas_right	iliopsoas muscle
48	quadriceps_femoris_left
49	quadriceps_femoris_right
50	thigh_medial_compartment_left
51	thigh_medial_compartment_right
52	thigh_posterior_compartment_left
53	thigh_posterior_compartment_right
54	sartorius_left
55	sartorius_right
56	brain

结论：

感谢各位小伙伴的点赞+关注，小易会继续努力分享，一起进步！