TotalSegmentator

Tool for segmentation of 104 classes in CT images. It was trained on a wide range of different CT images (different scanners, institutions, protocols,...) and therefore should work well on most images. The training dataset with 1204 subjects can be downloaded from Zenodo. You can also try the tool online at totalsegmentator.com.

Created by the department of Research and Analysis at University Hospital Basel.
If you use it please cite our paper: https://arxiv.org/abs/2208.05868. Please also cite nnUNet since TotalSegmentator is heavily based on it.

Installation

TotalSegmentator works on Ubuntu, Mac and Windows and on CPU and GPU (on CPU it is slow).

Install dependencies:

Python >= 3.7
Pytorch
if you use the option --preview you have to install xvfb (apt-get install xvfb)
You should not have any nnU-Net installation in your python environment since TotalSegmentator will install its own custom installation.
optionally: for faster resampling you can use cucim (pip install cupy-cuda11x cucim)

Install Totalsegmentator

pip install TotalSegmentator

Usage

TotalSegmentator -i ct.nii.gz -o segmentations

Note: Only nifti files are supported. To convert dicom files to nifti we recommend dcm2niix.

Note: If a CUDA compatible GPU is available TotalSegmentator will automatically use it. Otherwise it will use the CPU, which is a lot slower and should only be used with the --fast option.

Note: You can also try it online: www.totalsegmentator.com (supports dicom files)

Note: This is not a medical device and not intended for clinical usage.

Advanced settings

--fast: For faster runtime and less memory requirements use this option. It will run a lower resolution model (3mm instead of 1.5mm).
--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.
--roi_subset: Takes a space separated list of class names (e.g. spleen colon brain) and only saves those classes. Saves runtime during saving of nifti files.
--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 radiomics features of each class. You have to install pyradiomics to use this (pip install pyradiomics).

Subtasks

We added some more models to TotalSegmentator beyond the default one. This allows segmentation of even more classes in more detailed subparts of the image. First you have to run TotalSegmentator with the normal settings to get the normal masks. These masks are required to crop the image to a subregion on which the detailed model will run.

TotalSegmentator -i ct.nii.gz -o segmentations --fast
TotalSegmentator -i ct.nii.gz -o segmentations -ta lung_vessels

Overview of available subtasks and the classes which they contain.

Openly available:

lung_vessels: lung_vessels (cite paper), lung_trachea_bronchia
cerebral_bleed: intracerebral_hemorrhage
hip_implant: hip_implant
coronary_arteries: coronary_arteries
body: body, body_trunc, body_extremities, skin
pleural_pericard_effusion: pleural_effusion (cite paper), pericardial_effusion (cite paper)

Available after purchase of a license (free licenses available for academic projects). Contact jakob.wasserthal@usb.ch if you are interested:

bones_extremities: femur, patella, tibia, fibula, tarsal, metatarsal, phalanges_feet, humerus, ulna, radius, carpal, metacarpal, phalanges_hand, sternum, skull, spinal_cord
tissue_types: subcutaneous_fat, skeletal_muscle, torso_fat
heartchambers_highres: more precise heart chamber segmentation (trained on sub-millimeter resolution)
head: mandible, teeth, brainstem, subarachnoid_cavity, venous_sinuses, septum_pellucidum, cerebellum, caudate_nucleus, lentiform_nucleus, insular_cortex, internal_capsule, ventricle, central_sulcus, frontal_lobe, parietal_lobe, occipital_lobe, temporal_lobe, thalamus, tyroid (trained on sub-millimeter resolution)
aortic_branches: brachiocephalic_trunc, subclavian_artery_right, subclavian_artery_left, common_carotid_artery_right, common_carotid_artery_left, brachiocephalic_vein_left, brachiocephalic_vein_right, atrial_appendage_left, superior_vena_cava, pulmunary_vein, tyroid

Run via docker

We also provide a docker container which can be used the following way

docker run --gpus 'device=0' --ipc=host -v /absolute/path/to/my/data/directory:/tmp wasserth/totalsegmentator_container:master TotalSegmentator -i /tmp/ct.nii.gz -o /tmp/segmentations

Resource Requirements

Totalsegmentator has the following runtime and memory requirements (using a Nvidia RTX 3090 GPU):
(1.5mm is the normal model and 3mm is the --fast model)

If you want to reduce memory consumption you can use the following options:

--body_seg: This will crop the image to the body region before processing it
--force_split: This will split the image into 3 parts and process them one after another

Train / validation / test split

The exact split of the dataset can be found in the file meta.csv inside of the dataset. This was used for the validation in our paper.
The exact numbers of the results for the high resolution model (1.5mm) can be found here. The paper shows these numbers in the supplementary materials figure 11. To aggregate results across subjects and classes the following approach was taken: For each class in each subject calculate the (Dice) score, then take the average of all scores (micro averaging). If a class is not present on an image (e.g. the brain is not present on images of the legs) then exclude this value from the calculation.

Note: The model was trained on unblurred images. The published training dataset, however, has blurred faces for data privacy reasons. Therefore, models trained on the public dataset cannot be directly compared to our pretrained model. In the future we plan to provide a version of our model which was trained on the public blurred dataset so people can compare to this as a baseline.

Retrain model on your own

You have to download the data and then follow the instructions of nnU-Net how to train a nnU-Net. We trained a 3d_fullres model and the only adaptation to the default training is setting the number of epochs to 4000 and deactivating mirror data augmentation. The adapted trainer can be found here. For combining the single masks into one multilabel file you can use the function combine_masks_to_multilabel_file in totalsegmentator.libs.

Other commands

If you want to combine some subclasses (e.g. lung lobes) into one binary mask (e.g. entire lung) you can use the following command:

totalseg_combine_masks -i totalsegmentator_output_dir -o combined_mask.nii.gz -m lung

Install latest master branch (contains latest bug fixes)

pip install git+https://github.com/wasserth/TotalSegmentator.git

Typical problems

When you get the following error message

ITK ERROR: ITK only supports orthonormal direction cosines. No orthonormal definition found!

you should do

pip install SimpleITK==2.0.2

Reference

For more details see this paper https://arxiv.org/abs/2208.05868. If you use this tool please cite it as follows

Wasserthal J., Meyer M., Breit H., Cyriac J., Yang S., Segeroth M. TotalSegmentator: robust segmentation of 104 anatomical structures in CT images, 2022. URL: https://arxiv.org/abs/2208.05868.  arXiv: 2208.05868

Please also cite nnUNet since TotalSegmentator is heavily based on it.
Moreover, we would really appreciate if you let us know what you are using this tool for. You can also tell us what classes we should add in future releases. You can do so here.

Class details

The following table shows a list of all classes.

TA2 is a standardised way to name anatomy. Mostly the TotalSegmentator names follow this standard. For some classes they differ which you can see in the table below.

TotalSegmentator name	TA2 name
spleen
kidney_right
kidney_left
gallbladder
liver
stomach
aorta
inferior_vena_cava
portal_vein_and_splenic_vein	hepatic portal vein
pancreas
adrenal_gland_right	suprarenal gland
adrenal_gland_left	suprarenal gland
lung_upper_lobe_left	superior lobe of left lung
lung_lower_lobe_left	inferior lobe of left lung
lung_upper_lobe_right	superior lobe of right lung
lung_middle_lobe_right	middle lobe of right lung
lung_lower_lobe_right	inferior lobe of right lung
vertebrae_L5
vertebrae_L4
vertebrae_L3
vertebrae_L2
vertebrae_L1
vertebrae_T12
vertebrae_T11
vertebrae_T10
vertebrae_T9
vertebrae_T8
vertebrae_T7
vertebrae_T6
vertebrae_T5
vertebrae_T4
vertebrae_T3
vertebrae_T2
vertebrae_T1
vertebrae_C7
vertebrae_C6
vertebrae_C5
vertebrae_C4
vertebrae_C3
vertebrae_C2
vertebrae_C1
esophagus
trachea
heart_myocardium
heart_atrium_left
heart_ventricle_left
heart_atrium_right
heart_ventricle_right
pulmonary_artery	pulmonary arteries
brain
iliac_artery_left	common iliac artery
iliac_artery_right	common iliac artery
iliac_vena_left	common iliac vein
iliac_vena_right	common iliac vein
small_bowel	small intestine
duodenum
colon
rib_left_1
rib_left_2
rib_left_3
rib_left_4
rib_left_5
rib_left_6
rib_left_7
rib_left_8
rib_left_9
rib_left_10
rib_left_11
rib_left_12
rib_right_1
rib_right_2
rib_right_3
rib_right_4
rib_right_5
rib_right_6
rib_right_7
rib_right_8
rib_right_9
rib_right_10
rib_right_11
rib_right_12
scapula_left
scapula_right
clavicula_left	clavicle
clavicula_right	clavicle
hip_left	hip bone
hip_right	hip bone
sacrum
face
gluteus_maximus_left	gluteus maximus muscle
gluteus_maximus_right	gluteus maximus muscle
gluteus_medius_left	gluteus medius muscle
gluteus_medius_right	gluteus medius muscle
gluteus_minimus_left	gluteus minimus muscle
gluteus_minimus_right	gluteus minimus muscle
autochthon_left
autochthon_right
iliopsoas_left	iliopsoas muscle
iliopsoas_right	iliopsoas muscle
urinary_bladder
femur
patella
tibia
fibula
tarsal
metatarsal
phalanges_feet
humerus
ulna
radius
carpal
metacarpal
phalanges_hand
sternum
skull
subcutaneous_fat
skeletal_muscle
torso_fat
spinal_cord

basharbme/TotalSegmentator