ARTICLE IN PRESS

Original Investigation

Deep Learning-based Quantification

of Abdominal Subcutaneous and
Visceral Fat Volume on CT Images
Andrew T. Grainger, PhD, Arun Krishnaraj, MD, MPH, Michael H. Quinones, MD,
Nicholas J. Tustison, PhD, Samantha Epstein, MD, Daniela Fuller, BA, Aakash Jha, BA,
Kevin L. Allman, BA, Weibin Shi, MD, PhD

Rationale and Objectives: Develop a deep learning-based algorithm using the U-Net architecture to measure abdominal fat on computed
tomography (CT) images.
Materials and Methods: Sequential CT images spanning the abdominal region of seven subjects were manually segmented to calculate
subcutaneous fat (SAT) and visceral fat (VAT). The resulting segmentation maps of SAT and VAT were augmented using a template-based
data augmentation approach to create a large dataset for neural network training. Neural network performance was evaluated on both
sequential CT slices from three subjects and randomly selected CT images from the upper, central, and lower abdominal regions of 100
subjects.
Results: Both subcutaneous and abdominal cavity segmentation images created by the two methods were highly comparable with an
overall Dice similarity coefficient of 0.94. Pearson’s correlation coefficients between the subcutaneous and visceral fat volumes quantified
using the two methods were 0.99 and 0.99 and the overall percent residual squared error were 5.5% and 8.5%. Manual segmentation of
SAT and VAT on the 555 CT slices used for testing took approximately 46 hours while automated segmentation took approximately 1 min-
ute.
Conclusion: Our data demonstrates that deep learning methods utilizing a template-based data augmentation strategy can be employed
to accurately and rapidly quantify total abdominal SAT and VAT with a small number of training images.

Key Words: Deep learning; artificial intelligence; visceral fat; obesity.

© 2020 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Abbreviations: SAT subcutaneous fat, VAT visceral fat

INTRODUCTION historically been used to diagnose obesity. However, these

indirect measurements do not account for weight from skeletal

O
besity, defined as excessive fat accumulation in the
muscle, nor do they distinguish between differential fat distri-
body, is a growing global epidemic, with particular
butions such as visceral and subcutaneous fat. Distribution of
impact on the US population which has experienced
fat is a key variable when assessing obesity as greater distribu-
a marked increase in obesity levels over the last 50 years (1,2).
tion of visceral fat has been linked to more deleterious cardio-
Obesity is a public health problem due to its associated
vascular outcomes than total body fat or BMI alone (4 6).
increased risk for a variety of chronic diseases including meta-
Computed tomography (CT) is an imaging modality that
bolic syndrome, type 2 diabetes, cardiovascular diseases, and
permits easy distinction between fat and other tissues and thus
cancer (3). Anthropometric measurements such as body mass
allows for accurate measurement of fat and non-fat tissue
index (BMI), waist circumference, and waist-to-hip ratio have
amounts in the body (6). Quantification of body fat volume
using CT involves analysis of multiple slices across the region
Acad Radiol 2020; &:1–7 of interest, a laborious task if done manually, and hence not
From the Departments of Biochemistry & Molecular Genetics, Richmond, Vir- typically performed in routine CT interpretation.
ginia (A.T.G., W.S.); Radiology & Medical Imaging, School of Medicine, Virginia Deep learning using convolutional neural networks has
(A.K., M.H.Q., N.J.T., S.E., W.S.); School of Engineering and Applied Science,
University of Virginia, 480 Ray C. Hunt Drive, Charlottesville, VA 22908 (D.F., gained recent popularity in the literature for tackling prob-
A.J., K.L.A.). Received May 16, 2020; revised July 2, 2020; accepted July 6, lems in a multitude of areas, including image recognition,
2020. Address correspondence to: W.S. e-mail: ws4v@virginia.edu
classification and segmentation (7). Development of deep
© 2020 The Association of University Radiologists. Published by Elsevier Inc.
learning algorithms relies on large cohorts of training data to
All rights reserved.
https://doi.org/10.1016/j.acra.2020.07.010 identify important features of targets for predictions in new

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 ARTICLE IN PRESS
GRAINGER ET AL
data. To simultaneously expedite the process of CT segmen-
tation and quantification while reducing subjective influences
from observers, several semi and fully-automated algorithms
have been developed for quantifying body fat on CT (8 15).
However, nearly all of the previously published algorithms
are dependent on expert knowledge for tuning the features
of images or focus on a single or few slices within the abdom-
inal scan.
ANTsRNet is a collection of deep learning network archi-
tectures ported to the R language and built on the Keras
framework (16). We previously applied ANTsRNet to pro-
vide a comprehensive protocol for automatically segmenting
total abdominal subcutaneous adipose tissue (SAT) and vis-
ceral adipose tissue (VAT) using mouse Magnetic Resonance
images (17). This was accomplished through the use of a
novel technique designed by the Advanced Normalization
Tools team utilizing template-based data augmentation to
create a large training set using a small number of images.
Here, we have applied the same techniques to test the
hypothesis that deep learning using template-based data aug-
mentation could accurately and rapidly quantify total abdom-
inal SAT and VAT on human CT images. We have also
evaluated the relationship of SAT and VAT volumes with
BMI in a cohort.
METHODS
CT Images. 110 unique abdominal CT scans of 110 patients
(half men, half women), aged 60 § 16 years (19 93 years),
were randomly selected and retrieved through the Picture
Archiving and Communication System (PACS) at the Uni-
versity of Virginia. No exclusion or inclusion criteria were
used when selecting patients, as the goal was to develop an
algorithm that could properly segment any abdominal CT
image that it encountered. Scans used in this study were taken
from 2008 to 2019. Patient characteristics can be seen in
Table 1. The scan parameters varied among patients with a
tube current of 36»249 mA, slice thicknesses of 2.82 §
1.75 mm (1.25 5 mm), and a tube voltage of 120 kV. Aver-
age BMI was 28.1 § 0.8 kg/m2 (range: 17.2 52.9) for men
and 28.8 § 1.1 (range: 17.2 52.9) kg/m2 for women. This
large variation in tube current, slice thickness, and BMI was
chosen to ensure the algorithm could properly segment a
diverse set of CT images. Additionally, a few studies with
excessive artifacts were purposely included to test the ability
TABLE 1. Patient Characteristics
Factor Number
Male 55
Female 55
Age 60 § 16
BMI (Male) 28.1 § 0.8
BMI (Female) 28.8 § 1.1
Age and BMI are expressed as Mean § SD.
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Academic Radiology, Vol &, No &&, && 2020
to segment high-artifact images. All procedures were con-
ducted in compliance with the Health Insurance Portability
and Accountability Act and were included within an IRB
approved retrospective study protocol. CT images were de-
identified to protect patient identity.
Manual segmentation and quantification. No access to
semi-automatic segmentation programs was available for our
use, therefore the areas corresponding to the subcutaneous fat
in the abdominal cavity on each of the training CT images
were manually segmented by five coauthors on this article
using Image J (18). The coauthors who did the manual seg-
mentation had no medical background, but their work was
performed under the supervision of an experienced radiolo-
gist. Fat can be readily distinguished from non-fat tissues on
CT images in density, shape, and location. CT images were
adjusted through windowing on the PACS workstation to a
gray scale at which fat was visually distinguishable from non-
fat components (bone, air, background, soft, and watery tis-
sue). A bone window was found to be optimal in
distinguishing fat from non-fat tissues.
For quantification of fat, we developed an Image J-based
strategy using thresholding around a static intensity window
corresponding to fat on bone window-adjusted images. A
flowchart explaining the steps needed to quantify total fat can
be seen in Figure S1.
For segmentation of subcutaneous fat (SAT), we manually
outlined the area between the skin and the abdominal
muscles. Thresholding the image on specified values (82 97)
and quantifying the fat area within this selection represents
the SAT volume. Visceral fat (VAT) is defined as the fat
within the abdominal cavity. Due to its irregular shape and
extensive distribution in the abdominal cavity, VAT was dif-
ficult to manually segment. Therefore, the area correspond-
ing to the abdominal cavity was outlined and the VAT
volume was calculated though the quantification of fat within
this selection. Nonfat area was determined through thresh-
olding of the image so include all nonfat tissues (97 255).
Automatic Measurement. The creation of an automated
method for measurement of abdominal fat volume consists of
multiple steps, including training data preparation, template-
based data augmentation, and fat quantification. We
employed a strategy similar to the one previously used for
segmenting and quantifying abdominal fat of mice on MR
images (17). The complete flowchart of the process is shown
in Figure S2.
Template-Based Data Augmentation and Training: The
need for large training data sets is a known major limitation
associated with development of deep learning algorithms (7).
To achieve a training data set size that is sufficient for properly
segmenting total and subcutaneous fat, we employed a tem-
plate-based data augmentation strategy that we previously
used for segmenting abdominal fat of mice on MR images
(17). Multiple rounds of training were performed using an
increasing number of patients until we were satisfied that the
training weights could accurately segment the testing set. We
aimed to include the smallest number of patients possible to
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highlight the power of the template-based data augmentation
strategy that was used.
Six hundred and thirteen CT images covering the entire
abdominal region of seven individuals were selected for train-
ing. Of the seven subjects, two females and three males had a
normal BMI and one female and one male met BMI criteria
for obesity. Original CT images were adjusted at the PACS
to bone windows and saved as “.tiff” files. While DICOM
images work as well, “.tiff” files were chosen for training and
subsequent validation due to their reduced file size, the de-
identification of patient information while, and similar ease of
image saving. These images were converted to the Nifti (.nii.
gz) format using the ANTs toolkit (https://github.com/
ANTsX/ANTs). Each converted image was segmented into
two contoured areas, one for SAT and one for abdominal
muscle plus its encircled abdominal cavity, using the open
source segmentation tool ITK-SNAP and saved as a separate
segmentation image.
Training was performed using a U-net-based model and
with the ANTsRNet and Keras packages for R using a Ten-
sorflow backend, as was done previously (17).
Validation dataset: The accuracy of the deep learning-
based algorithm in segmenting subcutaneous fat was validated
with a group of images consisting of a combination of CT
images from three full abdominal scans taken from separate
subjects and randomly selected CT images for the upper, cen-
tral and lower abdominal regions of 100 subjects (555 total
images). The images from three full scans were chosen to val-
idate that the algorithm could properly segment images across
multiple individual scans. The images from 100 subjects were
included to validate that the algorithm could properly seg-
ment images from a diverse set of images from a diverse set of
individuals. Manual measurement results were used as the
ground truth for comparisons with the automated measure-
ment results. CT images were prepared as described above
and subsequently input into the trained U-net. Novel seg-
mentation images generated from the training were evaluated
for accuracy in quantification of SAT and VAT using a macro
developed for the Fiji package for Image J (19). The steps for
quantifying subcutaneous and visceral fat using the macro are
depicted in Figure S3.
Computational Time. Manual segmentation of total and sub-
cutaneous fat on the 555 images used in testing took
DEEP LEARNING FOR FAT QUANTIFICATION
approximately 46 hours compared to approximately 1 minute
using the deep learning-based algorithm for the same CT images.
Statistical Analysis. Comparisons were made between the
automated and manual methods in quantification of visceral
and subcutaneous fat volumes. The Dice metric was used to
determine the similarity between a manually generated seg-
mentation image and an automatically generated one. If two
segmentations completely overlap, the Dice score is 1; it is 0
if there is no overlap. This Dice score was determined using
the “Label Overlap Measures” function of the ANTs toolkit.
The residual was determined from the difference between
manually measured and automatically measured fat volume
for each slice. In addition, Pearson’s correlation analysis was
done to determine correlations between the manually and
automatically generated fat volumes and between fat volumes
and BMI, as reported (17). These residual and Pearson’s cor-
relation analyses were performed in R.
RESULTS
U-net-Based Deep Learning for Subcutaneous Fat Selection.
The U-net-based algorithm successfully generated the selec-
tions designating the subcutaneous fat region and the abdom-
inal cavity across an entire abdominal scan, and were highly
consistent with the manually generated selections created for
the same input images (Fig 1).
Comparison of Fat Volume Measured from Manual and
Deep Learning-Based Methods. Initial validation was done
on SAT volume measurements from the consecutive CT sli-
ces of three patients to determine whether the algorithm
could successfully generate segmentation images across an
entire abdominal scan. As shown in Figure 2a, SAT volumes
measured on sequential slices were comparable between the
two methods in all three patients. For each of these scans, the
total SAT volumes were also comparable between the two
methods (Fig 2b). The difference for scan 1 was 59,155 mm3
or 0.97% of the total volume, the difference for scan 2 was
692,520 mm3 or 5.4%, and the difference for scans 3 was
214,197 mm3 or 2.1% of the total volume. The average dif-
ference was 28,252 mm3 or 3.0% of the total volume.
Performance of the algorithm was further validated with CT
images from an additional 100 subjects randomly selected from
the University’s PACS database. One image was randomly
Figure 1. The accuracy of deep learning in
delineating areas containing subcutaneous
(SAT) and visceral fat (VAT) on CT images at
multiple levels. Representative images taken
every 20 slices from on of the three full scans
included in the validation dataset show consis-
tency between the manual and automatic
methods in segmenting SAT and VAT on CT
images. The red area denotes SAT and the
green area denotes VAT. Predicted segmenta-
tion: segmentation made by deep learning.
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Figure 2. Comparison between the automated and manual segmentation methods in quantification of SAT volumes. (a) Comparison of SAT
volumes measured from sequential CT images from upper (slice 1) to lower abdominal region of three individual subjects (black = subject 1,
red = subject 2, green = subject 3; solid = manual, hollow = automated). Each symbol represents an individual slice. (b) Comparison between
the manual and automated methods in measurements of total SAT volumes from three individual scans. (c) Bland-Altman Plot for all images in
the validation set (n = 555 images, 3 full scans + 3 images from 100 individuals). Each dot represents a single image. Orange solid line identifies
the mean difference between fat volumes caluclated using the manually generated or automatically generated segmentation images (m). Lower
solid red line identifies the Bland Altman lower limit of agreement (+2s), and upper red solid line identifies the Bland Altman upper limit of agree-
ment (-2s). (Color version of figure is available online.)

chosen from each of the upper, middle and lower abdominal
regions of an individual. For 12 CT slices, quantification of adi-
pose tissue compartments was impossible with the automated
method because subcutaneous fat area was discontinuous or the
muscle layer was incomplete. The image training did not
include images in which the SAT was discontinuous, and there-
fore the algorithm assumes a continuous SAT layer. When a
continuous SAT layer was not present, it artificially created one
and over-represented the area in which the SAT was predicted
to reside. A Bland-Altman plot combining the three full scans
and the remaining images from the 100 individuals shows a high
degree of accuracy for the predicted SAT volumes, with only
4.8% of the images being outside 2s from the mean (Fig 2c).
The volumes of VAT on sequential slices for the three full
scans were also comparable between the two methods (Fig 3a).
The difference between the total VAT volumes was also small
(Fig 3b). The difference for scan 1 was 59,155 mm3 or 2.7%,
the difference for scan 2 was 692,520 mm3 or 9.3%, and the dif-
ference for scans 3 was 214,197 mm3 or 5.3%. The average dif-
ference between fat volumes was 282,521 mm3, or 6.2%. A
Bland-Altman plot combining these three scans with the
additional 300 images from 100 individuals shows a high degree
of accuracy for predicted VAT volumes, with 4.8% of the
images being outside 2s from the mean (Fig 3c).
Pearson’s correlation was performed and residual squared
error was calculated on fat volume measurements for both
SAT and VAT for additional validation (Table 2). There was
a high degree of agreement between the SAT (R2 = 0.994,
p = 2.49E-217) and VAT (R2 = 0.989, p = 8.85E-193) vol-
umes quantified from predicted or manually-generated seg-
mentation images. The average residual squared error for
SAT was 5.494% and for VAT was 8.510%, further confirm-
ing the algorithm’s ability to accurately quantifies fat from all
images in an abdominal CT scan.
In addition to fat volume comparisons, Dice coefficient
values were calculated for the generated segmentation images
to measure the level of similarity in the images themselves.
The average Dice coefficient value was 0.94, suggesting a
high degree of similarity in selection shape and area (min
Dice = 0.80; max Dice = 0.98) (Table 2).
Correlations between Abdominal Fat Volumes and Body
Mass Index (BMI). Correlations of total, SAT and VAT

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Figure 3. Comparison between the automated and manual segmentation methods in quantification of VAT volumes. (a) Comparison of VAT vol-
umes measured from sequential CT images from upper (slice 1) to lower abdominal region of three individual subjects (black = subject 1, red = sub-
ject 2, green = subject 3; solid = manual, hollow = automated). Each symbol represents an individual slice (black = subject 1, red = subject 2,
green = subject 3; solid = manual, hollow = automated). (b) Comparison between the manual and automated methods in measurements of total VAT
volumes from three individual scans. (c) Bland-Altman Plot for all images in the validation set (n = 555 images, 3 full scans + 3 images from 100 indi-
viduals). Each dot represents a single image. Orange solid line identifies the mean difference between fat volumes caluclated using the manually
generated or automatically generated segmentation images (m). Lower solid red line identifies the Bland Altman lower limit of agreement (+2s), and
upper red solid line identifies the Bland Altman upper limit of agreement (-2s). (Color version of figure is available online.)

volumes with BMI were calculated using data from the above
validation cohort. Total fat volumes for the abdominal region
from the base of the lung to the pelvic brim (T12-L5) were
measured using the automated method, where visceral fat is
typically measured with CT (20,21). BMI was significantly
correlated with total (R2 = 0.145; p < 0.001) and SAT vol-
umes (R2 = 0.246; p < 0.001) (Figs 4a-b). There was no corre-
lation between BMI and VAT volume (R2 = 0.0134;
p = 0.144; Fig 4c). Because the amounts of abdominal fat vary
between individuals, fat volume was normalized by non-fat
mass for all subjects to account for the influence of abdominal
dimensions on individual variations in abdominal fat. After
normalization with nonfat mass, total fat showed an improved
association with BMI and SAT showed a reduced association
with BMI based on R2 and p values (Figs 4d-e). No correlation
was found between VAT volume and BMI (Fig 4f).
DISCUSSION
Our study successfully applies a deep learning-based approach
to the measurement of abdominal fat on CT scans that is
both accurate and rapid. Volumes of visceral and subcutane-
ous fat measured with our algorithm have shown a high
degree of consistency with those measured by the manual

TABLE 2. Validation of the Deep Learning-Based Algorithm for Accuracy in Quantitation of Subcutaneous (SAT) and Visceral Fat
(VAT) on CT Images

Average dice SAT SAT volume VAT VAT volume Percent RSE Percent RSE
value volume R2 p-value volume R2 p-value SAT volume VAT Volume

All 555 validation 0.944 § 0.002 0.994 2.49E-217 0.989 8.85E-193 5.494 8.510
images

The Dice score (mean § SE), correlation coefficients, and percent Residual Standard Error (RSE) are used for comparing the similarity of the
values of subcutaneous (SAT) and visceral fat (VAT) volumes measured by the manual and deep learning methods on the same CT images.

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Figure 4. Correlations of fat volumes quantified from all slices in the central abdominal region with BMI in a validation cohort of 100 patients.
Each point represents values of an individual subject. The correlation coefficient (R) and significance (P) are shown. a, b, c: Total, subcutane-
ous, and visceral fat volumes are expressed in real values calculated using the automated method. d, e, f, Total, subcutaneous, and visceral
fat volumes are normalized by dividing by nonfat volume on a same CT slice.

method, the current gold standard. By combining full
abdominal scans with a template-based data augmentation
strategy, we have successfully developed a unique method to
quantify total SAT and VAT while training on only a small
number of images. The ability to measure total body fat and
fat distribution is superior to common anthropometric meas-
urements such as BMI, waist circumference, and waist-hip
ratio which cannot accurately discern adipose tissue distribu-
tion in the body. Analysis of 100 abdominal CT scans shows
that BMI is moderately associated with subcutaneous fat vol-
ume but has no association with visceral fat volume.
A few deep learning-based methods to measure body fat
on CT scans have been reported (12 14). Compared to the
previous studies, our present study overcomes several limita-
tions. First, the inclusion of all CT slices in the abdominal
region was performed as compared to one or few slices used
in other studies. Fat distribution varies greatly in the abdomi-
nal region of obese subjects so obesity and overall fat content
may not be accurately reflected from one or few slices. Thus,
our method of including all CT slices should result in
improved precision and sensitivity for detecting change over
time in abdominal fat.
Second, our study employed a template-based data aug-
mentation strategy whereby images sampled were used to
construct a representative template that was optimal in terms
of both shape and intensity (22). This approach permits a sub-
stantial augmentation of the training dataset and overcomes
the limitation of deep learning in most cases which require
large-scale training datasets. Despite fewer CT slices being
used for the training, our algorithm has shown a comparable
performance to previous deep learning-based methods for
quantification of body fat using CT images (12 14).
Manually segmenting visceral fat on numerous CT slices
due to its irregular shape and extensive distribution within
the abdominal cavity is challenging. However, separating fat
from nonfat elements (air, background, waterish tissue, and
bone) is a more straightforward task. Thus, we chose to seg-
ment the abdominal cavity and use thresholding to isolate
and quantify the VAT. The chance of overestimating visceral
fat volume from other fat deposits such as bone marrow fat
and inter-muscular fat was minimal because the lumbar verte-
brae and pelvic bones are within the abdominal and pelvic
wall while visceral fat is located within the abdominal cavity.
Also, vertebrae and pelvic bones are cancellous bones con-
taining red bone marrow that have higher Hounsfield units
on CT than fat.
BMI is the most widely used measure of body adiposity in
clinical practice. The association of BMI with abdominal fat

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Academic Radiology, Vol &, No &&, && 2020
volumes directly measured by CT was tested in our cohort.
Our results demonstrate that BMI is only moderately associ-
ated with total abdominal and subcutaneous fat and has no
association with visceral fat. In studies of larger subjects, BMI
has also been found to be more highly correlated with subcu-
taneous fat versus visceral fat (20,23,24). These results suggest
that BMI is not a reliable marker of abdominal fat volumes
and is a poor proxy of visceral fat.
In summary, we have demonstrated the accuracy of our
deep learning based algorithm for quantifying abdominal fat
on CT scans. The algorithm has markedly expedited the pro-
cess of measuring abdominal fat volume allowing for poten-
tial routine reporting in the clinical setting. Moreover we
demonstrate the possibility of using a relatively small dataset
to effectively train a neural network to segment body fat.
This has important clinical implications as machine learning
can be readily applied to other regions or tissue types evalu-
ated on medical imaging. Despite the aforementioned advan-
ces afforded by applying deep learning to this task, the biggest
limitation is performance when an individual has a discontin-
uous subcutaneous fat layer. Another limitation is that we did
not analyze the inter-observer variation due to the laborious
nature of manual segmentation.
IRB STATEMENT
All procedures were conducted in compliance with the
Health Insurance Portability and Accountability Act and
were included within an IRB approved retrospective study
protocol (protocol #17041)
ACKNOWLEDGMENTS
Research reported in this publication was supported by the
National Institute of Diabetes and Digestive and Kidney Diseases
of the National Institutes of Health under Award Number
R01DK116768 and Commonwealth Health Research Board
(CHRB) Virginia. Andrew Grainger is a recipient of the Robert
R. Wagner Fellowship from the University of Virginia School of
Medicine. The work in this manuscript has not been published
partly or in full. The authors declare no competing interest.
COMPLIANCE WITH ETHICAL STANDARDS
The scientific guarantor of this publication is Weibin Shi at
the University of Virginia.
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SUPPLEMENTARY MATERIALS
Supplementary material associated with this article can be found
in the online version at doi:10.1016/j.acra.2020.07.010.