2020 6th International Conference on Advanced Computing & Communication Systems (ICACCS)
Spine Magnetic Resonance Image Segmentation
Using Deep Learning Techniques
J.Andrew Murathoti DivyaVarshini
Assistant Professor, B.Tech Student
Computer Science and Computer Science and
Engineering, Engineering,
Karunya Institute of Technology Karunya Institute of Technology
and Sciences and Sciences
Coimbatore, India. Coimbatore, India.
andrewj@karunya.edu divyavarshini28@gmail.com
Abstract—Spinal Malalignment is a chronic disease that is
widespread across the world. It causes different diseases such as
Stenosis, Scoliosis, Osteoporotic Fractures, Thoracolumbar
fractures, Disc degeneration, etc. The diagnosis of such disease is
generally done by analyzing the Magnetic Resonance Imaging
(MRI) scan of the lumbar spine region. MRI analysis is done by
well experienced medical professionals (radiologists and
orthopedists). The flip side to this inspection is that it is time-
consuming and may be subjected to a lack of accuracy. The
manual segmentation of MRI scans from a large number of scan
images is a tedious and time-consuming process. Thus, there is a
need for automatic segmentation and analysis of spine MRI scans
to improve clinical outputs and the accuracy of spinal
measurements. In recent, the rise of deep learning technologies is
making a revolution in medical systems. It is capable of analyzing
a large amount of data and yield better accuracy. So, deep
learning approaches can be efficiently used for the automatic
segmentation of MRI scans. In this paper, an overview of spinal
MRI segmentation using deep learning techniques is presented.
The disease diagnosis from spine MRI is conferred. Then the
state-of-art research in the automatic image segmentation using
Convolutional Neural Network (CNN) is discussed. A
comparative analysis is done on various deep learning techniques
based on the performance metrics is presented. Finally, the
evaluation metrics for automatic segmentation is provided along
with the comparison of the state-of-art results.
Keywords—CNN; MRI Segmentation; Spine MRI; Deep
Learning;
I. INTRODUCTION
Vertebral Misalignment is a disease caused by defects
present in the spinal region which comprises vertebral column
containing the cervical, the thoracic and the lumbar spine. The
vertebral column plays an important role in protecting the
spinal cord which comprises the central nervous system of our
body and it also gives support to the body. If there is any
damage in this region of the body the whole body stops
functioning properly, any damage in this area also causes
immense pain due to the large concentration of nerves. It is
divided into five parts, Lumbar vertebrae, is one of the
segments of the vertebral column whose function is to bear the
weight of the body. The lower vertebra endures most weight
978-1-7281-5197-7/20/$31.00 ©2020 IEEE
Prerna Barjo Irene Tigga
B.Tech Student B.Tech Student
Computer Science and Computer Science and
Engineering, Engineering,
Karunya Institute of Karunya Institute of
Technology and Sciences Technology and Sciences
Coimbatore, India Coimbatore, India.
prernabarjo@karunya.edu.in tiggairene@gmail.com
as compared to the other portions. The five lumbar
vertebrae(L1-L5) is the largest vertebrae in the vertebral
column, making it strong enough to support the weight of the
upper portion of the human body. This structure keeps all the
bones, joints, nerves, ligaments, and the muscles intact, each
of them contributing to supporting, strengthening and
maintaining the body’s flexibility [1].
Back pain comes under the most prevalent common health
problems in the world. Such problems in the lower back may
be caused by innumerable circumstances which can be
problems such as irritation or the spine structures
malalignment. These abnormalities in the lower back such as
an uncomplicated muscle strain and osteoporotic fractures
might cause serious problems that may require emergency
medical treatment, whereas some problems such as disc
degeneration and scoliosis will cause pain and may be treated
by physical therapy [2]. MRIs are the most used LSS
inspection tool to diagnose defects in the patient’s spine [3].
The radiologists who inspect these medical images require
years of expertise in this field and in some cases, the diagnosis
may be subjected to inaccuracy [4]. Thus, to build a
Computer-Aided Diagnosis (CAD) system, accurate
calculation procedures have to be observed, considering there
are various methods to compute the measurements [5].
Therefore, the development of an automated spinal alignment
analysis tool will provide timely medical results without the
need of taking an appointment [6].
Segmentation plays an important role in the diagnosis of
spinal MRI scans and if done manually may take a lot of time
and require experience. Feature extraction is necessary to
generate ground truth label images for training purposes.
Although this method is also subjected to possible
inaccuracies, considering the region of interest is very small
which is difficult to bound yet the advances in the technology
will provide better solutions in the near future [7]. There are
numerous classification models that provide specific
segmentation of the spine and correct diagnosis of diseases
[8].
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Fig. 1. Block Diagram of Spine MRI Segmentation Techniques and Disease Prediction
II. SPINAL MALALIGNMENT IDENTIFICATION THROUGH MRI
Segmentation of MRI helps the physicians to detect various
spinal malalignments such as Stenosis, Scoliosis, Osteoporotic
Fractures, Thoracolumbar Fractures, and Degeneration.
Stenosis [9]- Lumbar spinal stenosis [10] refers to the
narrowing of the spinal canal which occurs due to continuous
impact on the tissues located between the vertebrae causing
inflammation, and pain in the spinal nerves. This causes
Chronic Lower Back Pain (CLBP) which leads to various
other complications that may require surgical treatments.
Scoliosis [11] – Scoliosis is the abnormal curve in the
spine, this condition may cause an increase in curve which
causes the structure to deform into S-shape or C- shape curve
[12]. This is caused due to intense level of physical activity,
neurological defects, and birth defects. The Curvature
estimation may be used to calculate the extremity in the spine
deformation [13]. Cobb angle detection is the most effective
way of calculation of curvature of the spine.
Osteoporotic Fractures [14] – Osteoporosis is degradation
of the bone density which is developed along with time with
the weakening of bones. This makes the bones very fragile and
more prone to fractures. OVF is mostly found in elderly
people around the age of 80 due to the degeneration of bones.
Thoracolumbar Fractures [15]- Thoracolumbar spine
injuries are injuries borne to Thoracic and Lumbar vertebrae
[16]. These are induced by a heavy impact on the back such as
a hard fall, road accidents or physical trauma. This can be
found in patients of any age range.
Degeneration [17] - Disc degeneration is weakening of
bones due to gradual aging [18]. The quantification of disc
degeneration requires the detection of MRI scans. MRI texture
is observed to check the biological and physical tissue
properties used to set a part of the pathological and normal
status in a vast area of clinical applications.
A. Feature Extraction using MRI
Feature extraction is done to extract the features from a
segmented image of MRI scans and transforming the
completely available image data into feature sets [19].
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Extraction plays a major role, where effective features are
extracted provides a higher rate of accuracy. Mainly
classification of the image is divided into two and
unsupervised and supervised. The supervised learning
techniques involve information classes, and the dataset has to
be divided into two namely training and test dataset [20].
While unsupervised learning methods [12] are fast but they
might be inaccurate because they don’t have example data to
learn from.
III. SPINE MRI SEGMENTATION
Segmentation of images is a fundamental process of
analyzing an image [10]. It is the method of forming minor
segments from the image to identify various elements
necessary for the analysis process. Spinal Disorders are the
most common in this current world. MRI and CT scans are
image modalities used for manually identifying the defected
vertebrae. But this manual process is a laborious one. And it’s
very challenging to detect the vertebrae and identify the pose
of the vertebrae. Performing this task manually requires
expertise and its time consuming too. So, automation [21] is
highly demanded in this field [18]. After the origination of the
convolutional neural network (CNN) [22], many efforts have
been taken to utilize CNNs for numerous image segmentation
tasks. Precisely, CNN has led to deep learning approaches
[23] where algorithms automatically learn characteristic
features from raw data at multiple different levels of
abstraction to perform classification tasks at a high level of
performance.
A. Manual Segmentation
Manual Segmentation of spine MRI scans requires
experts in the spine image interpretation [24]. Radiologist has
to go through multiple slices of MRI images and diagnoses
every region of spine and performs manual sketching in the
defective region [3]. It can be very challenging to segregate
the object from the MRI scans. This process is time-
consuming and requires more effort, as it is done by observing
spatial and axial scans together, checking temporal profiles
and hence probing numerous series of enhanced data and
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contours of pixels while determining the boundary of the
lesion.
B. Automatic Segmentation
Automatic segmentation is a process by
which segment boundaries are allocated automatically by a
program. There are many benefits to automatic segmentation
of the spine using MRI scans. It increases efficiency,
decreases repetitive tasks, and the elimination of
inconsistencies like inter and intraobserver variance [25].
However, automatic segmentation of the spine is highly
challenging considering the high similarity of structural
features [26] in each slice, and difficulty in differentiating
between vertebrae’s morphological structure and surrounding.
IV. DEEP LEARNING BASED IMAGE SEGMENTATION
TECHNIQUES
There are different types of image segmentation techniques
particularly in Deep Neural Network to achieve pixel-wise
segmentation [1]. Multiple architectures can be selected for
the network: SegNet it uses encoder-decoder architecture for
layer-wise segmentation [27], NoPoolASPP has a
convolutional neural network including feature layer with
filters at various sampling rates resulting in effective
segmentation thus capturing objects and their image context at
multiple scales [28], U-Net demonstrates the state-of-the-art
results on the grey matter segmentation challenge [24],
DeepLab [27] is dilated convolution network whereas
RefineNet goes through downscaling which not beneficial in
the case of segmentation.
Fig. 2. The segmentation and processing of MRI scans
A. Patch Based Segmentation
In patch-based classification [29] approach image
segmentation is done to differentiate between the Anterior and
Posterior part of the vertebrae section of the spine. The width
of the AAP varies from location where the measurement of the
spine is taken. This approach uses the Image Input Layer and
Convolution Layers. When the input is given for processing
then the Image Input layer receives each pixel in patch and
data normalization is applied. In the next step, the resultant
data is fed to the Convolution Layers. Each layer has equal-
sized kernels with a classification feature trained in them. To
increase the speed of the training of segmentation batch
normalization is applied on layers and activation function
ReLu (Rectified Linear Unit) is applied to train networks. At
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the end of this process, fully connected layers are used to
extract the features. Finally, classification is done through the
Softmax classifier.
B. Segnet Based Segmentation
Another deep learning approach namely SegNet is explored
[27] which comprises a sequence of convolution layers
formulated in encoder-decoder architecture. The objective of
encoder layers is to select the image features at varying
resolutions and boundary detail is its final output. Firstly, the
input is fed into convolution layers with filter banks in each
layer, the result is fed to batch normalization and the ReLu
activation function is applied. Subsampling is done using max
pooling. The process of restoring, upsampling of the output
signal using the max-pooling layer is done in the decoder. The
result is fed to the convolutional layer using filters, batch
normalization, and ReLu activation function. Finally, softmax
function is applied and the resulting output is segmented
image.
C. SVM+HOG Methodology Based Segmentation
Support Vector Machine(SVM) is a supervised learning
algorithm used for segmentation, in this method of
segmentation, tight bounding boxes are formed to encapsulate
the region of interest for all visible discs in the upper vertebrae
in mid-sagittal MRI image. The Histogram of oriented
gradients (HOG) methodology is a state-of-art image
classification which is followed by image segmentation [30].
Firstly, the discs are segmented based on corresponding axial
MRIs that are calculated from the intersection of the axial
slices with the Sagittal. Then segmentation of the leftover
discs was done using a two-stage classifier. In these steps,
HOG features and SVM features are used.
D. U-Net Based Segmentation
U-Net is a fully convolutional neural network which is
particularly used for segmentation [31]. Segmentation of the
Vertebral Disc the segmentation network is trained to detect
the discs from the image dataset. The similarity between the
MRI scans of different disk cause confusion therefore, a
bounding box is used to crop the estimated center. Then they
are zero-padded so they can be well fed into the convolutional
network. To increase the accuracy of the network ReLU
activation function is used in the 3D convolution network and
dropout operation is added.
E. Alexnet Based Segmentation
In this approach, AlexNet deep CNN model [25] is used
to refine the boundary. The Active Appearance Model (AAM)
assists as the initial level of the segmentation pipeline.
Initially, atlas-based AAM provides a rough bounding area for
the deep learning model. This rough boundary is then passed
through the modification process from the atlas-based AAM
model at the secondary level. This procedure is a pixel-based
segmentation for 2-D patch-based pixel classification.
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TABLE I.EVALUATION OF SEGMENTATION TECHNIQUES BASED ON PERFORMANCE METRICS
Reference MRI Image Type Segmentation Technique Measurement Standards Performance Metrics
[7] local PACS of the lumbar or the CNN Euclidean distance Accuracy 96.5%
cervical spine.

[18] lateral view cervical spine Random Forest Mean and S.D 95% accuracy. Sensitivity. 98%
radiographs. specificity. 93%
[1] CT scans of the abdomen, chest, and ResNet34 model with two FC Adam optimizer Accuracy of 89.2% sensitivity
pelvis region. layers of 85.2% specificity of 95.8%
[5] 35 lumbar MRI scans SVM, PCA+LDA, PCA+Naive Normalized GLCM Gn Accuracy of 94.85% specificity
Bayes, PCA+QDA,PCA+SVM of 95.9% sensitivity of 92.45%

[8] CT and MRI scans of Normal KNN Euclidean distance Accuracy 86.13 % sensitivity
(100 patients) or Abnormal (210 90.24% specificity 77.50%
patients). precision 89.48%
[10] MRI scans of sagittal view and axial HOG+SVM Deviation of disc centers Nil
discs view. (Deveu) (in mm) Accuracy
Deviation of Percent Disc
pixels (DPD) OutPercent
(Outper)
[12] X-ray images of spinal cord. U-Net DSC,JS,MSE, accuracy, Accuracy 96.9 sensitivity 98.2
Dense U-Net sensitivity,and specificity specificity 95.8
Residual U-Net

[25] MRI scans of prostate gland. Patch-Based CNN, AlexNet: DSC, IoU, HDRFDST, DSC 89.77%
HNN architeture AVGDIST. Jaccard similarity coefficient
(IoU) of 81.59%
[32] both sagittal and axial scans. HOGsupervised descent method Jaccard coefficient, or the Accuracy of 95.6%
(SDM)CNN regressor. Intersection over Union performance (%) 73.9
(IoU),
[33] 200 sagittal MR slices from 42 U-Net DSI based loss function is Vertebrae DSI scores 0.865
patients. Multi-pixel segmentation used to evaluate the accuracy Disks DSI scores 0.832

TABLE II. COMPARISON OF SEGMENTATION METHODS

Reference Year Dataset Objective Segmentation Methods

[34] 2016 Spineweb , Groupwise registration and multi-modal feature TDCN + SVM
MS Annotated Spine CT fusion.
Database

[7] 2017 (MNIST) dataset Two separate detection pipelines are CNN
constructed

[10] 2012 Private dataset Effective labelling of intervertebral discs. HOG+SVM

[5] 2011 Private database 5-fold cross-validation is performed SVM, PCA+LDA, PCA+Naive Bayes,
PCA+QDA,PCA+SVM

[32] 2017 Genodisc, TwinsUK, and To perform automated radiological gradings in HOG, SDM, CNN regressor.
OSCLMRIC Lumbar spine MRI’s

[12] 2019 MRI images from hospital. provides a reliable assessment of scoliosis. U-Net, Dense U-Net, Residual U-Net,

[1] 2018 DHMC Improving the OVF diagnosis. ResNet34 model with two FC layers

[8] 2018 Kaggle and UCI machine Detection of most significant KNN
learning database Abnormalities in spine.

[24] 2020 MNIST AND CIFAR-10 Facilitating accurate and mobile alignment Mask R-CNN
detection.

[18] 2016 Private dataset Uses x-rays to detect degenerative change in Random forest
the cervical spine.

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 2020 6th International Conference on Advanced Computing & Communication Systems (ICACCS)

that SVM performs better in comparison. Through this study,

V. EVALUATION METRICS it has been observed that a vast majority of image
Various evaluation metrics are used to determine the classification in the field of spinal malalignment detection has
competency of the algorithm used in the segmentation of the experimented upon the SVM classifier. Different pre-trained
images. As it is already seen that many different classifiers can models such as SegNet, AlexNet, and U-Net, HOG, Contour
be used for the execution of the process it makes it a very model and Patch-based pixel classification were studied and
crucial task to evaluate the efficiency of each algorithm given compared to concludes to which method is the best. The
each algorithm has its own benefits only a few can be used in comparison of these methods was based on observing
this given context. While comparing these methods it is also performance metrics such as Specificity, Sensitivity,
important to consider the time utilized to compute the given IOU(Intersection over Union), Accuracy, Dice Coefficient
data, which is an important measure of efficiency. To measure (DC), Precision among others.
this Jaccard Index is used, or intersection-over union of class c
TABLE III. PERFORMANCE METRICS COMPARISION
[10] after the segmentation is done it is compared with the
ground truth value which is already given and the pixel-based Techniques Accuracy Specificity Sensitivity
similarity is calculated where ݉௖௖ is the correctly predicted
pixel count of class c, ‫ݐ‬௖ is the total number of pixel with TDCN+SVM 98.1% 92.1 93.8
respect to the ground truth and ݉௖ is the number of pixels CNN 98.8% 99.6 99.1
predicted to belong to class c.
୫ౙౙ
݅‫ݑ݋‬௖  ൌ (1) SVM, PCA+LDA, 94.86% 95.9% 92.45%
୲ౙ ା୫ౙ ି୫ౙౙ PCA+Naive
The performance metrics namely specificity, sensitivity and Bayes,PCA+QDA,PCA
precision provide us with precise values which effectively +SVM
compare the algorithms, their formulas are as follows:
்ே௦ U-Net, Dense U-Net, 96.9 95.8 98.2
Specificity =
்ே௦ାி௉௦
(2) Residual U-Net

ResNet34 with two FC 89.2 85.2 95.8

்௉௦ layers
Sensitivity = (3)
்௉௦ାிே௦
KNN 86.13 % 90.24% 77.50%
்௉௦
Precision = (4)
்௉௦ାி௉௦ Random Forest 95% 98% 93%

Specificity measure also known true negatives which VII. CONCLUSION

correctly predicts the false classes or without disease in the
given dataset. Sensitivity also known as true positives which
correctly predicts the cases with diseases in the given
dataset.A precision measure considers all the positives and
calculates the accuracy of prediction within the true positives.
TN stands for True Negatives, FN stands for False Negatives,
TP stands for True Positives and FP stands for False Positives.
Accuracy is the percentage of correctly segmented disc
centers. The formula for accuracy is:
்௉ା்ே
Accuracy = (5)
்௉ା்ேାி௉ାிே
VI. INFERENCE & DISCUSSION
For the detection of spinal diseases, the normal course of
action is to acquire MRI and CT scans for the patients
concerned. Manual analysis can sometimes be inaccurate
which calls for an automatic analysis of the same. Automatic
segmentation will enable the production of clinical outputs
with more accurate measurements. For this purpose, a deep
learning approach is implemented which is known as
Convolutional Neural Network (CNN). It was have
experimented with different classifiers and it was observed
Spinal malalignment causes serious health issues if not
diagnosed at earlier stages. MRI scans play a major role in the
detection and diagnosis of spinal malalignment. The MRI scan
images are segmented to identify disorders. The manual
prediction of spinal disorders in the MRI scans is laborious
and might produce inaccurate results. This emphasizes the
need for the implementation of automatic segmentation
techniques of the spinal MRI. This paper comprises a survey
on various deep learning methodologies such as SegNet, U-
Net, and AlexNet among others. The U-Net architecture is
better designed as compared to other algorithms since it works
with fewer training images and it produces more accurate
segmentation. However, automatic segmentation has its
limitations such as analyzing a large amount of data to train
the network model. A comparison of these architectures is
done using standard evaluation metrics such as accuracy,
precision, sensitivity, and specificity. This will assist in
choosing the best algorithm for spinal MRI segmentation. In
the future, experimental studies can be done on these
algorithms for improving medical results. Integrating these
deep learning techniques with the medical apparatus will help
us to take a giant leap towards greater medical advancements.

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 2020 6th International Conference on Advanced Computing & Communication Systems (ICACCS)
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