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Bioinformatics
doi.10.1093/bioinformatics/xxxxxx
Advance Access Publication Date: Day Month Year
Manuscript Category

Bioimage Informatics

aXonica - A Magnetic Resonance Imaging Solution

Bilal Wajid 1 , Hasan Iqbal 1,∗ , Momina Jamil 1 , Faria Anwar 2 , Ramoona Latif 1 ,
Tayyaba Asif 1 and Arslan Khan 1
1
Department of Electrical Engineering, Istanbul Commerce University, Istanbul, Turkey and
2
Mayo Hospital, Lahore, Pakistan.
∗ To whom correspondence should be addressed.
Associate Editor: XXXXXXX
Received on XXXXX; revised on XXXXX; accepted on XXXXX

Abstract
Motivation: Magnetic Resonance Imaging (MRI) is a radiological test which employs powerful magnets,
radio waves and computational analysis in order to make a detailed image of an individual’s internal organs
and tissue, thereby facilitating the diagnosis of a vast range of medical conditions including cancer. MRI
scan generates large amounts of raw data which need to be carefully handled, reconstructed and proces-
sed. Volume rendering, 2D and 3D visualization, morphometric analysis, modelization, diffusion analysis
and perfusion analysis enables the radiologists to easily and precisely pinpoint the anomaly and compare
it with several references. Image processing and analyses are rendered easy with the aid of an entire sof-
tware pipeline which requires researcher to have prior knowledge of scripting, operating systems (such as
Linux), installing and maintaining software with varying dependencies most of which are not user-friendly
and lack basic GUI. This indeed is an inconvenience for researchers in life-sciences as they are spending
increased amount of time simply maintaining software rather than conducting actual research work. The-
refore, in order to facilitate MRI sciences, this paper present ‘aXonica,’ a Graphical User Interface (GUI)
based installation and interactive application package encompassing forty-two tools stretching the entire
length of the software pipeline aiming to optimize the development of software workstations needed for
MRI-based Neuroimaging analysis.
Results: aXonica implements a Ubuntu-based package which facilitates the installation of forty-two sof-
tware related to MRI along with a separate GUI based application to run each tool.
Availability: aXonica is available at https://github.com/hasaniqbal777/aXonica
Contact: hasaniqbal777@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.

1 Introduction
Magnetic Resonance Imaging (MRI) is a non-invasive imaging techno-
logy that produces detailed anatomical images by using strong magnetic
fields, gradients, and radio waves. However, due to the use of strong
magnetic fields, MRI cannot be performed on patients with iron-based
metal implants (Katti et al., 2011). Nevertheless, MRI images are speci-
ally important in the diagnosis of brain and spinal cord injuries, multiple
sclerosis, cancer and stroke (Aswathy et al., 2014; McDonald and Sadow-
sky, 2002; Barkhof et al., 1997; Chen et al., 2007; Hentschel et al., 2011;
Igarashi, 2007). Moreover, MRI images are employed to assess the health
of different organs, for instance, breasts and ovaries of women, prostate
for men and liver, kidneys and pancreas for both males and females.
MRI scanner produces large amounts of raw data which need to be
processed and diagnosed. The raw data along with images in frequency-
domain are reconstructed into time-domain (Hansen and Kellman, 2015).
These images are further prepared for precise and accurate diagnosis.
This data processing is made possible using computational techniques.
Therefore, in order to translate this biological data into relevant clinical
information, researchers have proposed several software along the entire
pipeline. These software not only helped speed up clinical diagnosis and
research, but also compelled biologists to spend increasing amount of time
and resources in installing, configuring and maintaining software. More-
over, most of these software do not provide a graphical user interface but

© The Author 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 1

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2 Bilal Wajid et al.

rather assume that the users are comfortable with scripting. An assum-
ption, which in reality does not hold true or does not account for most
of the users in life-sciences. Therefore, in order to ease the installation of
MRI-based software this paper presents ’aXonica,’ an installation package
geared towards Neuroimaging.
5. Structural Analysis Installs tools categorized in (a) Modeling,(b)
Brain Connectomics, (c) Morphometric Analysis, (d) Quality Control,
(e)Classification, (f) 3-D Image analysis and (g) Mapping.
6. Data Management and Annotation: Install tools classified under
(a) DICOM file management and (b) Format Management.

In reference to the execution of the installed tools, the authors employed

2 Methods
aXonica encompasses software geared towards Magnetic Resonance Ima-
ging (MRI), specifically Neuroimaging. Therefore, the developers ensured
that all avenues of MRI-based Neuroimaging are covered within the analy-
sis pipeline. Figure 1 shows the MRI-based Neuroimaging pipeline and
lists all the software, and their download sizes, present within the proposed
solution.
The choice of software was determined via the following criteria:
• Publication date after 2010
• Freeware License
• Linux based
• Offline
For the sake of brevity the complete table and the application of the
selection criterion is shown in the Table 2 in the Supplementary section.
This report shows details of the final set of tools present within aXonica,
as shown in Figure 1 and Table 2.
The authors employed "Zenity" as the front-end GUI for users so that
they have an easy and user friendly interface for installation of these forty-
two tools. However, linux bash scripting was employed to carefully handle
each installation including necessary dependencies to ensure the users are
able to develop workstations quickly and easily. The dependencies which
are necessary for the installation of other tools are mentioned herein below
and are automatically installed during the execution of aXonica:
• JAVA JDK 8
• python and python3
• Scipy
• Numpy
• python-pip and python-pip3
• PyQt4
• PyQtgraph
• PyOpenGL
• h5py
In essence aXonica is designed using a couple of shell executable files
(with front-end Zentiy based GUIs) concatenated with one another each
containing a number of commands that download and install necessary
software based upon user’s input. The shell files are enlisted herein below:
Qt framework to develop a GUI through which the user get access to all
installed software simply by clicking interactive buttons. The developed
GUI does indicate the list of all available tools in aXonica. At the same
time the GUI also disables the buttons of those tools which the user decided
not to install.
3 Results and Discussion
aXonica was developed with the intention to facilitate the deployment
of software workstations and laboratories for MRI diagnosis and resea-
rch. Among the vast scope of MRI’s use, the authors chose to focus on
Neuroimaging thereby concentrating their attention on software related to
diagnosis of the brain and spinal cord. The selection criterion mentioned
in Table 1 of Supplementary Section filtered most of the software retaining
about 42 tools which are encompassed by aXonica installation package.
All these tools are mentioned in Table 2 and Fig. 1 along with their relative
sizes. MATLAB plug-ins are also not included because MATLAB is a paid
software and require license. These software are mentioned in Table 2 of
Supplementary Section.
Moreover, as most users are expected to belong from life-sciences aXo-
nica bypasses the command-line interface by providing a Zenity based GUI
in order to facilitate the users during the installation process (see Figure
2) and a QT based GUI (see Figure 3) in starting different software along
the analysis pipeline.
In order to ensure the robustness and longevity of aXonica developers
verified the installation process on Ubuntu 16.04 LTS, with end of life date
(EOFD): April 2021 and Ubuntu 18.04 LTS (EOFD: April 2028). Table 1
shows the testing and verification environment.
Table 1: This list shows the hardware and software configuration of the
systems on which aXonica was tested and verified.
Configuration 1
Processor Intel Core i7-3630QM, 6M Cache, up to 3.40 GHz
RAM 8GB
Hard Disk 256GB SSD
Graphics NVIDIA GeForce GT 640M, 2GB
Operating System Ubuntu 16.04 LTS 64 bit
Configuration 2

Processor Intel Core i7-7500U, 4M Cache, up to 3.50 GHz

1. Internet Availability: An active internet connection is needed to
RAM 8GB
start the process. Therefore, this first executable shell file checks the
system for an active internet connection and terminates the installation Hard Disk 256GB SSD
process if internet connection is not available. Graphics Dedicated Intel HD Graphics 620
2. Dependencies Installation: The dependencies mentioned above are Operating System Ubuntu 18.04 LTS 64 bit
downloaded and installed.
3. Pre-Processing: This shell file allows the user to automatically
install tools related to (a) Visualization, (b) Enhancement and (c)
Reconstruction.
4. Processing: Install tools based upon (a) Registration, (b) Segmenta-
tion and (c) Surfacing.

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aXonica 3

Fig. 1: The figure presents an overview of the MRI data analysis pipeline. The software tools packaged in aXonica, along with their size are mentioned
along each category in the figure (Riviere et al. (2003), Garyfallidis et al. (2014), Doube et al. (2010), Fogal and Krüger (2010), Loening and Gambhir
(2003), Loening and Gambhir (2003), Griffa et al. (2010), Chang et al. (2009), Ou et al. (2018), Li et al. (2017), Yushkevich et al. (2006), Eklund et al.
(2017), Craddock et al. (2012), Lesjak et al. (2015), Arganda-Carreras et al. (2006), Yoo et al. (2002), Delgado-Gonzalo et al. (2012), Eskildsen et al.
(2012), Gulban et al. (2018), Lancaster et al. (2012), Natale et al. (2011), Cointepas et al. (2001), Schirner et al. (2016), Bazin et al. (2014), Hines et al.
(2009), Barbier et al. (2017), Bekolay et al. (2014), Gleeson et al. (2007), Stimberg et al. (2017), Loula et al. (2017), Karperien (2013),
López-Fernández et al. (2016), Schindelin et al. (2015), Gorgolewski et al. (2011), Prodanov and Verstreken (2012), de Moraes et al. (2011), Kesler
et al. (2011), McAuliffe et al. (2001), Valeri et al. (2015))

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4 Bilal Wajid et al.

Furthermore, the developers will continue to update aXonica in order to 18 Segmentator (Gulban et al., 2018) 1.7 0.19.1
incorporate latest software tools. Additionally, the supplementary section Image Registration
contains the following:
19 Mango (Lancaster et al., 2012) 67 1.7.0
• Table for Selection criterion of software 20 bunwarpJ (Natale et al., 2011) 0.2 2.6.5
• Table for MATLAB Plug-ins which are not included
• Installation Instructions Image Surfacing
• Information about Data Acquisition and Software Pipeline
21 BrainVISA (Cointepas et al., 2001) 1100 4.5.0
• Download instructions for tutorial data-sets
• Sample examples for each step in the pipeline Structural Analysis
• Usage of aXonica_UI application
• Instruction to execute each tool Brain Connectomics

22 The Virtual Brain (Schirner et al., 670 1.5.4

2016)
Table 2: The table enumerates software packaged in aXonica in 23 CBS Tools (Bazin et al., 2014) 147 3.1.0
accordance with their categories. 24 HagaEtAl2017 (Haga and Fukai, 0.1 1.0.0
2017)
25 NEURON (Hines et al., 2009, 2008) 8 7.5.0
Sr. Software 26 SliceMap (Barbier et al., 2017) 44 1.0.0
Software Name Size (MB)
No. Version 27 Nengo (Bekolay et al., 2014) 38 2.8.0
28 neuroConstruct (Gleeson et al., 0.4 1.6.0
Pre-processing 2007)
29 MedInria (Toussaint et al., 2007) 58 2.2.3
Image Visualization 30 BRIAN (Stimberg et al., 2017) 68 2.0.2
31 Timedomain decoding (Loula et al., 0.5 1.0.0
1 Anatomist (Riviere et al., 2003) N-A 4.5.0
2017)
2 Dipy (Garyfallidis et al., 2014) 30 0.15.0
3 BoneJ (Doube et al., 2010) 0.7 1.0.0 Morphometric Analysis
4 ImageVIS3D (Fogal and Krüger, 30.9 3.1.0
2010) 32 FracLac (Karperien, 2013) 13.8 1.0.0
33 Gwyddion (Nečas and Klapetek, 50 2.44.1
Image Enhancement 2012)
5 AMIDE (Loening and Gambhir, 40 1.0.4 Image Classification
2003)
6 PID (Griffa et al., 2010) 5.1 1.12.0 34 LA-iMageS (López-Fernández 298 1.1.5
7 TORTOISE (Chang et al., 2009) 751.5 3.1.0 et al., 2016)
8 NormalizeFOV (Ou et al., 2018) 732 1.2.0 3D Image Analysis
9 FastFilter3D (Li et al., 2017) 0.3 1.0.0
35 Brainstorm (Tadel et al., 2011) 76.6 3.0.0
3D Image Reconstruction 36 ImageJ (Schindelin et al., 2015) 137.7 2.0.0
37 nipype (Gorgolewski et al., 2011) 48 1.1.7
10 ITK-SNAP (Yushkevich et al., 45.2 3.6.0
2006) Image Mapping
Processing 38 MRI-Processor (Prodanov and 0.5 1.0.0
Verstreken, 2012)
Image Segmentation
Data Management and Annotation
11 HeteroscedasticfMRI (Eklund et al., 0.19 1.0.0
2017) Format Management
12 pyClusterROI (Craddock et al., 0.4 1.0.0
2012) 39 NiBabel (de Moraes et al., 2011) 48 2.3.1
13 BrainSeg3D (Lesjak et al., 2015) 18.5 1.0.0 40 MRIcron (Kesler et al., 2011) 24.5 1.0.0
14 CMP-BIA (Arganda-Carreras et al., 0.1 0.3.0 DICOM File Management
2006)
15 ITK (Yoo et al., 2002) 88 3.4.7 41 MIPAV (McAuliffe et al., 2001) 134 8.0.2
16 E-Snake (Delgado-Gonzalo et al., 0.1 1.0.0 42 Weasis (Valeri et al., 2015) 19 3.0.4
2012)
17 mincBEAST (Eskildsen et al., 1.96 1.15.0
2012)

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aXonica 5

(a) Welcome Screen (b) Internet Availability Screen (c) Dependencies Installation Screen

(d) Pre-processing Tools Selection Screen (e) Processing Tools Selection Screen (f) Structural Analysis Tools Selection Screen

(g) Format Management Tools Selection Screen (h) Finalizing Installation Screen

Fig. 2: The figure shows the dialog boxes which appear during the installation process. The Installation begins by the (a) Welcome Screen and (b)
checking the internet connection. If the system is connected installation of aXonica begins by first (c) installing dependencies followed by (d)
pre-processing, (e) processing, (f) structural analysis and (g) format management tools, completing the process by showing the (h) finish screen.

4 Conclusion 5 Availability and Requirements

This paper presents aXonica, a solution comprised of a GUI-based instal- aXonica is available and downloadable as follows:
lation package consisting of forty-two MRI image analysis software along
• Project Name: aXonica
with an additional GUI application facilitating the user to run installed
• Current Version: v3.1
software. aXonica is freely available under GPL v3.0 license, via github.
• URL: https://github.com/hasaniqbal777/aXonica
It comes with a detailed supplementary section encompassing tutorial
• Operating System: Ubuntu 16.04 LTS, Ubuntu 18.04 LTS
data-sets, version history and a step-by-step guide with instructions on
• Checked on: 15 January 2019
installation and use of different software. Moreover, to ensure longevity of
• License: GNU General Public License (GPL v3.0)
aXonica, authors tested and verified its running on both on Ubuntu 16.04
• Internet Connection: Required
and 18.04 LTS. Lastly, the authors intend to continuously update aXonica
• Contact: hasaniqbal777@gmail.com
with latest software in order to keep it relevant for several years to come.
• Note: Administrative privileges are required to install the software.

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6 Bilal Wajid et al.
(a) Main Step Selection Screen
(b) Pre-processing Selection screen
(c) Tool selection screen
Fig. 3: The figure shows the application boxes which the user will
interact with in order to use installed software. They include (a) selecting
the primary analysis paradigm followed by (b) choosing the main
categories and finally (c) deciding which particular software to run
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