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D. S.

DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015

Comparison of air trapping(AT) identification in


Computed Tomography(CT) in expiration scans
using different threshold levels
Diogo da Silva Dias, dias.5@wright.edu, UID U00777095, Processing of Medical Images, Wright
State University,Spring 2015, March 23rd, 2015, Professor: Mr. Nasser Kashou,

AbstractGoal: This study intends to evaluate which


Threshold criteria is the best when using only expiratory scan.
Methods: In order to do this some thresholds were chosen in
literature to compare it`s efficacy of identifying and quantifying
AT with a radiologist analysis of a child expiratory state scan.
through using segmentation and computer vision techniques in
MATLAB Results: It was found that the threshold between -850
and -910 HU was the closest to the radiologist analysis and that
the child could be suffering of a mild chronic obstructive
pulmonary disease. Conclusion: . The methodology used showed
potential to quantify AT without inspiratory scans showing
potential to reduce radiation dose in patients and it`s required
further studies with more subjects for statistical analysis, and the
use of more segmentation techniques like vessel removal and
analysis of each lung lobes separately. Significance: There is no
consensus yet on which thresholds for quantifying AT is/are the
best in this application, .
Index Terms Air Trapping,
Tomography, Expiratory Scan.
I.

Threshold,

Computer

INTRODUCTION

A. Background

HE evolution of Computed Tomography(CT) imaging


systems is highly relevant on lungs imaging, modern CT
systems are able to image 64 1-milimiter slices during a 1second rotation of its gantry. This evolution has came out with
a new range of applications and a large amount of data for the
radiologists to analyze, this situation suggested that this
process of analysis could be automated, or offer help to the
radiologists with computer vision tools [1]. The CT imaging
resolution can be acquired at a submilimiter level, allowing
direct visualization in changes of small airways of 2mm, and
even more advanced CTs like multi-detector ones that can
detect intrapulmonary and endobronchial structures of
0.2mm3[1-3].
One thing that these higher resolution CT scans could detect
and quantify is air trapping(AT) that is defined as retention of
air during expiration state of the lungs[1,2]. particularly at the
level of small bronchial tubes. Expiratory CT scans by
themselves are able to detect AT according to Gaeta et al
(2013)[4].

Basically the procedure of acquiring the expiratory CT


scans is typically obtained at the end of a forced expiration.
During the scan the patients are advised to : Take a deep
breath, blow out hard, and do not breathe in again for 10
seconds. It's required that each patient practice it before the
scanning begins[4].
The majority of quantitative CT techniques to measure AT
are density based ones, like: comparing expiratory to
expiratory ratio of mean lung density; and volume change of
voxels between two threshold of Hounsfield units(HU)[3-9])
and percentage of voxels below-856 HU in a expiratory
scan[9]. Some of them also compare or associate the CT scans
with pulmonary functional tests[2,3,6,7].
B. Significance
AT is related to various airways obstruction in several
diseases like emphysema, bronchiolitis obliterans, bronchial
asthma, Swyer-James syndrome,reactive airway disease,
cystic fibrosis, bronchiectasis, sarcoidosis, hypersensitivity
pneumonitis, atypical pneumonia and eosinophilic granuloma
[4,10]. Early AT measurements and detection is also important
for finding diseases in their early stages like chronic lung
rejection[2], smoking-related lung cancer, chronic obstructive
pulmonary disease(COPD)(Mets et al 2012) and small airways
disease. An early finding of these diseases are essential
because there could be an interventions in their early stages
which could prevent their progression and their severity.
According to some studies there is no consensus or standard
on how to quantify AT.[5,8], But in order to standardize and
universalize the protocols we need, there is a problem because
there is no agreement between studies due different scanner
models; reconstruction algorithms, parameters protocols(voxel
size, tube voltage (kVp), and tube current, exposure time
product (mAs),number ) interpatient variation in inspiratory
and expiratory lung volumes, the degree of expiration at the
time of the scanning and the threshold techniques during AT
finding.[9,10].
Despite most of authors say that we need both expiratory
and inspiratory CT scans for lung disease, this approach is
questionable because the amount of radiation exposed to the
patient during the acquisition mainly for patients undergoing
repeated exposures and young patients[4](that is the case of
this study).There is even a study[10] that discuss that using
tube current time down to 20mAs it`s possible to gather AT
information without imparing it.

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015


C. Hypothesis
Comparing AT finding and quantifying criteria and
techniques is a way of trying to standardize and further create
consensual protocols for clinical application.
D. Purpose
The purpose of this study is to compare different threshold
criteria in expiratory scan some studies for finding and
quantifying AT regions and find which one have closer results
to the radiologist findings on the same scans.
II.

METHODS

A. DICOM headers
In this project I had for analysis 4 lung scans in expiratory
state and in DICOM format, and the 4 same scans with the
indication of AT regions by radiologists. Using the command
dicominfo() of MATLAB I could gather some information
on how the scans were acquired and it is showed on table 1, in
order to help me interpret the data I used a guidance
document(ACR, 2013), and this other one. Reading the dicom
files of each header I realized the 4 scans were from the same
person, this person was a male child.
TABLE 1
INFORMATION OF THE ACQUISITION OF THE IMAGES IN THE DICOM HEADERS
OF THE FILES

Some Dicom Files Headers information


HISPEED RP CT system
System
from GE
512x512
Resolution
16
Bit Depth
"Grayscale"
Color Type
5 years old
Patient`s Age
Male
Patient`s Sex
1mm
Nominal Slice thickness
120
KVP(Kilo Voltage peak)
used
100
Tube current(mA)
1000
Exposure time (ms)
100
Current exposure time
250
Reconstruction
Diameter(mm)
-1024
[b]Rescale Intercept
1
[m]Rescale Slope
B. Thresholding criteria
After that reading the dicom header of the files, I`ve
followed some ideas of the procedures of some analogue
studies, like the automated isolation of the lungs from the
parenchyma, [1,2,5,7,8]; separate the left from right lung
[8,11] and the use of threshold techniques for detecting
AT[2,3,6,7,8,11]. The threshold levels of HU in some
studies(....) used for expiratory state is showed on table 2,
analyzing these studies, It was possible to define 5 thresholds
for AT detection(A,B,C,D and E), in the studies without the
Lower Level will be defined as -1024 because it is the rescale

2
intercept value .
TABLE 2 THRESHOLD LEVELS IN EXPIRATORY CT FOR DETECTING AT

Threshol
d range

Colormap

Solyanik et
al 2013[2]

Cohen et al
2008[3]
Lee et al
2008[6]
Schrodder
et al
2013[9]
Zach et al
2013[12]
Mets et al
2012[8]

Spring
(pink,
yellow)
Autumn
(red,yello
w)

Bommart
et al
2014[5]
Radiologist
`s analysis

Upper
level(H
U)
-750

Lower
Level(H
U)
-910

-950

Winter
(blue,
green)

-856

Summer
(Green,
yellow)
Hot
(red,
white)
Grayscale/
yellow
line
marker

-860

-950

-850

-910

C. Converting raw data to Hounsfield Units(HU)


In order to make this a quantity analysis using HU I had
to convert the raw data into HU and for doing a DICOM
manual [12] gives the instructions on how to do it, there is a
formula (eq. 1) using the rescale intercept[b] and slope[m] to
convert the raw data[SV] into HU.
Output units = m(SV) + b; (1)
D. Image Analysis Through code
Using the previous considerations I wrote a m-file in
MATLAB R2014a for measuring and displaying the AT
region on a CT scan of the expiratory state, called
ATmeasure(). there is a diagram (Fig.1) and a example (Fig.
2) of on how the code works in Appendix 1. The procedure of
ATmeasure() has the following steps:
1- Reading the DICOM image and storing it in a raw data
array(Fig 2.a) and a converting dicom image in another
uint16 array(Fig 1.b).
2- Isolating automatically the lungs from other tissues in the
uint16 image and each lung in different arrays(Fig 2. d)
3- Creating and applying masks to each lung with the
function maskcreator() that`s going to be commented
further.( (Fig 2.e)

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015


4- Converting the raw data into HU with eq. 1 and storing
the converted data in other array
5- Applying the previously created mask for each lung in
the AT array.
6- Highlighting the places in the lungs with AT within the
inputted threshold by the user.(Fig.2.f)
7- Creating another mask with the AT regions for each
lung.(Fig 2,g)
8- Calculating the percentage of AT and the mean
attenuation in HU of each lung, and then printing these
results on the command window
9- Plotting the image of the lungs with the Highlighted AT
regions.
The maskcreator() is a function used by ATmeasure(), it
has a diagram (Fig.3) and a example(Fig. 4) on Appendix 2 to
illustrate how the code works. During this code development, I
had huge help from Shoelson`s webinar videos at
www.mathworks.com, on how to create masks in MATLAB
and on how to use the MATLAB`s built-in function
regionprops()[13,14].The procedure of maskcreator() has the
following steps:
1- Loading a uint16 array (Fig 4.a)
2- Adjusting the uint16 histogram and creating a Black
and white binary image out of the grayscale one,
making black areas with intensities in one peak of the
histogram and white the regions on the other
peak.(Fig 4.b)
3- Using regionprops() for finding "areas" on the Black
and white image
4- Making all the areas black except the biggest one, in
the case of this application the lung. (Fig 4.c)
5- Filling the "holes" in the image with imfill()(Fig 4.d)
6- Making this resultant mask as the output of the
function.
E. Comparison
In order to check the difference between the thresholds I
used different colormaps(Table 2) for each threshold result
and I`ve compared then with the radiologist findings, to
evaluate which threshold was closer to the radiologist
findings. The percentage of AT in each scan for each lung as
well their mean lung attenuation were put in tables, to evaluate
the quantification of the AT.

III. RESULTS
On Table 3 below the Mean Lung attenuation of the 4
available slices of the CT scan in the expiratory stage is
showed below, the left and right lung are observed separately

3
TABLE 3
MEAN LUNG ATTENUATION(HU) IN EACH LUNG IN 4 SLICES

Slice
1
2
3
4
Average

Left Lung(HU)
-739.03
-726.2
-779.94
-746.33
-747.8822.94

Right Lung(HU)
-737.35
-725.39
-781.64
-748.03
-748.124.19

There is not a huge difference in the mean lung attenuation


of the lungs according table 3.
Comparing the Mean Lung attenuation in expiratory state
in table 3 to Schrodder et al (2013)[8] results we could say
that this subject can have a mild(-730.4) to moderate(-758.8)
COPD. However we should consider that the age group was
different from our subject, maybe his case could have a
different severity.
On Table 4 In Appendix 3 shows the percentage of the AT
in relation to the lung area is showed, for every slice, for each
Table 2`s thresholding criteria, for each lung separately. In
order to compliment this table Figures 5,6,7 and 8 in
Appendix 3 show the visual differences between the
techniques and the radiologist analysis of where the AT is.
Observing Table 4 and figures 5-8 in appendix 3 it looks
that the thresholds A and B, are not good for this application,
A for detecting more AT than the previewed by the
Radiologists and B for almost not detecting AT at all.
Comparing C,D and E percentages of AT in expiratory state to
the Schrodder et al 2013 [8] results, it`s reinforced the idea
that the subject has a a mild COPD.
Despites the radiologist points out the regions on the CTs
where there is AT. Looking at the table, thresholds, C, D and
E had very close AT percentage measurements and looking at
the figures 5-8 the threshold E is the closest one to shows the
AT detection similar to the Radiologist analysis, we could say
that maybe this threshold is better to evaluate the existence of
AT in young children, or Males.
Between thresholding criteria C,D and E, closer criteria to
the radiologist analysis, it was not seen a big difference of left
and right lung of as in table 3
IV. CONCLUSION
It was possible to create a MATLAB code to detect AT
quantifications and position similar to the radiologist findings
mainly in using a threshold of -950 and -850 HU as Bommart
et al(2014)[5] for detecting AT, as I had only one subject no
statistical analysis could be made like[2,6,8] this is study was
also limited having only the expiratory state, but as it was
possible to quantify AT without Inspiratory state it`s possible
to say that it was not a major problem of this study and besides
it, this result confirms the idea that it`s questionable the use of
Inspiration state for AT quantification and identification and
we could also reduce patient`s dose for this applications if we
keep developing a protocol for quantifying AT only with
Expiratory CT scans.

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015


Other improvements that further studies could have
besides more subjects and consequently statistical analysis, is
analyzing lung lobes segmentation, lung vessels removal,
having a better interface in the software to the user as
suggested by Summer et al. (2006)[1].One other possibility is
testing the technique of this study using even of lower
radiation dose in acquiring the images as said by Bankier et
al (2007)[10].

REFERENCES
[1] I. Sluimer, A. Schilham, M. Prokop and B. van Ginneken.
Computer analysis of computed tomography scans of the
lung: A survey. Medical Imaging, IEEE Transactions
on 25(4), pp. 385-405. 2006.
[2] O. Solyanik, S. Dettmer, T. Kaireit, F. Wacker, H.-O.
Shin; Detection of pathologic air trapping in patients after
lung transplantation: comparison of three methods using
Multi Detector Row CT.ECR 2013,2013.
[3] J. Cohen, W. R. Douma, P. M. van Ooijen, T. P. Willems,
V. Dicken, J. M. Kuhnigk, N. H. ten Hacken, D. S.
Postma and M. Oudkerk. Localization and quantification
of regional and segmental air trapping in asthma. J.
Comput. Assist. Tomogr. 32(4), pp. 562-569. 2008.
[4] M. Gaeta, F. Minutoli, G. Girbino, A. Murabito, C.
Benedetto, R. Contiguglia, P. Ruggeri and S. Privitera.
Expiratory CT scan in patients with normal inspiratory
CT scan: A finding of obliterative bronchiolitis and other
causes of bronchiolar obstruction. Multidiscip Respir
Med 8pp. 1-86. 2013.
[5] S. Bommart, G. Marin, A. Bourdin, N. Molinari, F. Klein,
M. Hayot, I. Vachier, P. Chanez, J. Mercier and H.
Vernhet-Kovacsik. Relationship between CT air trapping
criteria and lung function in small airway impairment
quantification. BMC Pulmonary Medicine 14(1), pp. 29.
2014.
[6] Y. K. Lee, Y. Oh, J. Lee, E. K. Kim, J. H. Lee, N. Kim, J.
B. Seo, S. Do Lee and KOLD Study Group. Quantitative
assessment of emphysema, air trapping, and airway
thickening on computed tomography. Lung 186(3), pp.
157-165. 2008.

4
[7] O. M. Mets, P. Zanen, J. J. Lammers, I. Isgum, H. A.
Gietema, B. van Ginneken, M. Prokop and P. A. de Jong.
Early identification of small airways disease on lung
cancer screening CT: Comparison of current air trapping
measures. Lung 190(6), pp. 629-633. 2012.
[8] J. D. Schroeder, A. S. McKenzie, J. A. Zach, C. G.
Wilson, D. Curran-Everett, D. S. Stinson, J. D. Newell Jr
and D. A. Lynch. Relationships between airflow
obstruction and quantitative CT measurements of
emphysema, air trapping, and airways in subjects with
and without chronic obstructive pulmonary disease. AJR
Am. J. Roentgenol. 201(3), pp. W460-70. 2013.
[9] M. L. Goris, H. J. Zhu, F. Blankenberg, F. Chan and T. E.
Robinson. An automated approach to quantitative air
trapping measurements in mild cystic fibrosis. CHEST
Journal 123(5), pp. 1655-1663. 2003.
[10] A. A. Bankier, C. Schaefer-Prokop, V. De Maertelaer, D.
Tack, P. Jaksch, W. Klepetko and P. A. Gevenois. Air
trapping: Comparison of standard-dose and simulated
low-dose
thin-section
CT
techniques
1. Radiology 242(3), pp. 898-906. 2007.
[11] J. A. Zach, J. D. Newell Jr, J. Schroeder, J. R. Murphy,
D. Curran-Everett, E. A. Hoffman, P. M. Westgate, M. K.
Han, E. K. Silverman, J. D. Crapo, D. A. Lynch and
COPDGene Investigators. Quantitative computed
tomography of the lungs and airways in healthy
nonsmoking adults. Invest. Radiol. 47(10), pp. 596-602.
2012.
[12] NEMA.National Electrical Manufacturers Association.
Digital Imaging and Communications in Medicine
(DICOM). Part 3: Information Object Definitions .
Virginia, 2011.
[13] B. Shoelson.Webinar:Medical Imaging Workflows with
MATLAB.Mathworks.2011.
Available
at
:
http://www.mathworks.com/videos/medical-imagingworkflows-with-matlab-81850.html
[14] B. Shoelson.Webinar:Medical Image Processing with
MATLAB
.Mathworks.2011.
Available
at:
http://www.mathworks.com/videos/medical-imageprocessing-with-matlab-81890.html

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015

Appendix 1

Fig.1 - The Diagram of the ATmeasure() function

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015


Appendix 1

Fig.2 - The Steps of the ATmeasure() function.a-) is the raw data, b-) is the adjusted imagee, c-) is the image without other
structures near the lungs, d-) is the left lung separeted, e-) is the lung after using the mask, f-) is the AT mask without being
filtered, g-) is the left lung with the AT measuremenst highlighted.
Code 1 - ATmeasure().m
%% ATmeasure()
% Diogo Dias UID# U00777095
% BME 7112 Processing of Medical Images
% Spring 2015
% Midterm Project
%
%% --- help for ATmeasure() --%
% ATmeasure() is a function that reads a Dicom CT Image of a Segment of the lungs
% in a expiration state, then calculates the percentage of air trapping(AT)
% in each lung and the mean attenuation in Hounsfiled units(HU) in each
% lung as well, it also plot a grayscale image of the lungs with the AT.
% The procedure follows
% 1- It reads the image
% 2- It creates and apply masks to each lung
% 3- It highlights the places in the original image with a threshold
% inputted by the user
% 4- It creates another mask with the AT regions
% 5- It calculates the percentage of AT and the mean attenuation in HU of
% each lung, and then print it in the command window
% 6- It plots the image of each
%% Function Start

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015


%
%
%
%
%
%

PATleft and PATright are the percentage of AT in each lung


meanHousleft and meanHousright is the mean attenuation in housfield in
the lungs
lower ATT is the lower threshold for finding the AT
upper ATT is the upper threshold for finding the AT
A2 is the matrix with the highlighted

function[PATleft, PATright, meanHousleft, meanHousright, A2] = ATmeasure(lowerATT,


upperATT)
%% Start a clean state
close all;clc;%close all;
%set(0,'DefaultFigureWindowStyle','docked');
%% Open image, change its format and contrast
%cd ['C:\Users\Diogo\Documents\backup hd externo\WSU\Processing of Medical ...
%'Imaging\Midterm project'];
%B = dicomread('IM1');
%I use the built-in function dicomread()
B = dicomread(uigetfile({'IM*'},'Pick a CT file'));
%imshow(B) %procedure check 1
A = uint16(B);
%imshow(A);%procedure check 2
A1 = imadjust(A);
%imshow(A1)%procedure check 3 I`ve used this image to check out what coordinates I
would use
%to remove the regions above and below the lung from the image in
%the next cell
%% Remove image parts below and above the lung
%I would do it to make it easier to create a mask for the lungs
A1(1:110,:)= 0 ;
A1(350:end,:)= 0 ;
A1(A1 >= 35000) = 0;
%imshow(A1);%procedure check 4
%% Divide the lungs into two arrays
Aleft = A1;
Aright = A1;
Aleft(:,267:end) = 0;%make right lung black
Aright(:,1:267) = 0;%make leftt lung black
%imshow(Aleft);%procedure check 5
%% Create masks for each lung
%I use here a function called maskcreator that I`ve wrote myself to create
%the masks, the comments about is done in this function itself.
leftmask = maskcreator(Aleft);
rightmask = maskcreator(Aright);
%imshow(leftmask);%procedure check 6
%% Apply Masks
%The following code will make everything outside the masks with intensity 0
%i.e black
Aleft(~leftmask) = 0;
Aright(~rightmask) = 0;

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015


%imshow(Aleft);%procedure check 7
%% Checkout Air Trapping regions
% to come up with this cell of code I`ve read the header of the dicom files
% to check the rescale slope and intercept to convert the raw data of the
% dicom file into HU
m = 1; %rescale slope
RI = -1024; %rescale intercept
%lowerATT = -910; %Air Trapping Threshhold
%upperATT = -750;%According to cohen et al 2008;
B(B == -32768) = -300;
B = B.*m + RI; %slope for conversion
meanB = B;
B(B > lowerATT & B < upperATT) = 10000; %make the regions with Air Trapping Whiter
%imshow(B)%procedure check 8
B1 = uint16(B);%turn the values into uint16
bwb1 = ~im2bw(B1 <10000);% Make the values other than the Air trapping
%values into black and AT region values into white
leftATT = bwb1;
rightATT = bwb1;
leftATT(~leftmask) = 0;%applying the left lung mask
rightATT(~rightmask) = 0;%applying the right lung mask
leftATT = imfill(leftATT,'holes');
rightATT = imfill(rightATT,'holes');
%imshow(leftATT + rightATT);
%% Apllying the AT masks
Aright(rightATT)=65535;%make the Air trapping region of the right lung white
Aleft(leftATT) = 65535;%make the Air trapping region of the left lung white
%imshow(Aleft)%procedure check 9
%figure(2)
%imshow(Aleft);
%% percentage of AT
%calculating the percentage of the lung with AT
PATleft = nnz(leftATT)/nnz(leftmask);
PATright = nnz(rightATT)/nnz(rightmask);
fprintf([' The percentage of Air trapping of the left lung is %0.2f\n and'...
'the right lung is %0.2f\n'], PATleft, PATright);
%% mean Attenuation of the lung
meanHousleft = mean(meanB(~leftmask));
meanHousright = mean(meanB(~rightmask));
fprintf([' The average attenuation in Hounsfield units(HU) in the left'...
'lung, %3.2f\n is and the right lung is %3.2f\n'],...
meanHousleft, meanHousright);
%% unite lungs
A2 = Aleft + Aright;
figure(3);
imshow(A2(100:400,50:450));%plot only the lungs region
title('Air Trapping Measurement Done');
%% Function end

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015


clear all;
end% function end
Appendix 2

Fig.3 - The Diagram of the maskcreator() function

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015

Fig.4 - The Steps of the maskcreator() function.a-) is the segmented left lung, b-) is the image in black and white, c-) is the
biggest area of the image obtained through regionprops , d-) is the resultant mask.
Code 2 - maskcreator().m
%% maskcreator()
% Diogo Dias UID# U00777095
% BME 7112 Processing of Medical Images
% Spring 2015
% Midterm Project
%
%% --- help for maskcreator() --%
% maskcreator() is a function that gets grayscale image and creates a mask
% only for the biggest object in it.It uses regionprops built-in MATLAB`s function
% and its Area feature. The 'image' is the grayscale image and [mask]
% is the resultant mask
% In this code I would like to cite and thank Brett Shoelson`s webinar videos
% at www.mathworks.com("Medical Imaging Workflows with MATLAB" and
% "Medical Image Processing with MATLAB" both recorded on April 2012) that
% gave me ideas for creating masks, and helped a lot in this midterm project.
%% The code itself
function[mask] = maskcreator(image)

10

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015

11

%according to graythresh`s help it uses the Otsu's method, which chooses


%the threshold to minimize the intraclass variance of the thresholded
%black and white pixels.
G = graythresh(image);
%im2bw converts the intensity values into black for values that are below
% the threshhold G and white to values above G
BW = im2bw(image,G);
%imshow(BW);%procedure check 10
%bwconncomp is a function that stores the properties of a black and white
%matrix, it`s going to be used further in the code
cc = bwconncomp(BW);
%regionprops with the Area flag return All the areas that the region props
%could find in the Black and White image
stats = regionprops(BW,'Area');
S = [stats.Area];
%the maximum area in the figure is selected in this code to be used as a
%theshold to make it 0 all the other areas out of the bigger one.
[~,tresh] = max(S);
BW(labelmatrix(cc)~= tresh)= 0;
%imshow(BW);%procedure check 11
%imfill () built-in function that makes the mask smoothier without holes on
%it
BW = imfill(BW,'holes');
mask = BW;
%imshow(BW);%procedure check 12
end %function end

Appendix 3
TABLE 4 - PERCENTAGE OF DETECTED AT IN THE RIGHT AND LEFT LUNG, WITH THE DIFFERENT THRESHOLD CRITERIA

Threshold
Range
A
B
C
D
E

Slice 1
Left
Right
Lung(%)
Lung(%)
54
68
1
1
19
19
16
16
16
15

Slice 2
Left
Right
Lung(%)
Lung(%)
46
30
0
0
5
4
4
3
5
4

Slice 3
Left
Right
Lung(%)
Lung(%)
74
44
0
0
9
6
8
5
8
5

Slice 4
Left
Right
Lung(%)
Lung(%)
63
42
0
0
8
5
7
4
9
5

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015

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Fig.5 - The Different Thresholds for detecting AT and the Radiologist analysis ,analyzing the slice 1,.a-)Threshold between -750
HU -910 b-) Threshold between -950 HU -1024 c-) Threshold between -856 HU -1024
d-) Threshold between -860 HU -950e-) Threshold between -850 HU -910.f-) radiologist analysis.

Fig.6 - The Different Thresholds for detecting AT and the Radiologist analysis ,analyzing the slice 2,.a-)Threshold between -750
HU -910 b-) Threshold between -950 HU -1024 c-) Threshold between -856 HU -1024
d-) Threshold between -860 HU -950e-) Threshold between -850 HU -910.f-) radiologist analysis.

D. S. DIAS, BME 7112, MIDTERM PROJECT, SPRING 2015

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Fig.7 - The Different Thresholds for detecting AT and the Radiologist analysis ,analyzing the slice 3,.a-)Threshold between -750
HU -910 b-) Threshold between -950 HU -1024 c-) Threshold between -856 HU -1024
d-) Threshold between -860 HU -950e-) Threshold between -850 HU -910.f-) radiologist analysis.

Fig.8 - The Different Thresholds for detecting AT and the Radiologist analysis ,analyzing the slice 4,.a-)Threshold between -750
HU -910 b-) Threshold between -950 HU -1024 c-) Threshold between -856 HU -1024
d-) Threshold between -860 HU -950e-) Threshold between -850 HU -910.f-) radiologist analysis.