Brain Connectivity From Diffusion MRI Tractography for

Psychotic Disorder Diagnostic

Outlines

● Introduction
● Diffusion magnetic resonance imaging
● Tractography
● Deterministic algorithms
● Probabilistic algorithms
● Tractograms filtering
● Brain network analysis for diagnosis
● Programs
● References
Introduction
The intricate networks of the human nervous system have received a lot of attention recently, especially the cerebral
cortex, which is made up of about 10^10 neurons arranged in local circuits and long-distance connections. The
human connectome project is the result of research on this network.

In this context diffusion MRI has proven to be a useful tool for the millimeter-scale investigation of brain axonal
networks since it can probe the tissue microstructure in vivo and non-invasively. Diffusion MRI makes it possible to
map a low-resolution estimate of the human connectome, which could revitalize research on healthy or abnormal
neuroanatomy, allowing for the reconstruction of the white matter connections in the brain on a large scale, offering a
crucial tool for quantitatively mapping the structural connections of the brain utilizing connectivity or tissue
microstructure measurements.

In order to quantitatively analyze the anatomical connections of the brain in both health and disease, tractography is
used. Where dMRI tractography is now a crucial technique for research on a variety of brain illnesses, such as but not
limited to: schizophrenia, depression, obsessive-compulsive disorder (OCD), attention-deficit hyperactivity disorder
(ADHD) and autism [1,2].

Following a brief introduction to tractography—the method for reconstructing fiber tracts from diffusion images—and
diffusion MRI, we will introduce the different tractography algorithms; Deterministic algorithms and probabilistic
algorithms utilizing the monte carlo method. And finish with two quantitative tractography analyses methods,
tract-specific analysis, which denotes research that often follows a hypothesis and examines specific anatomical fiber
tracts, and connectome-based analysis.
Diffusion magnetic resonance imaging
The diffusion magnetic resonance imaging was introduced in the mid-1980s and has
become one of the most important modern neuroimaging techniques. Diffusion MRI
reveals the microarchitecture in the brain by measuring the random motion of water
molecules in brain tissues. Diffusion MRI has many clinical applications, such as the
diagnosis of acute brain stroke. It can also produce astonishing maps of white matter
tracts in the brain, with the potential to aid the understanding of psychiatric disorders and
improve brain tumor radiation therapy planning
Diffusion MRI provides unique possibilities to study structural connectivity of the human
brain, e.g. how the white matter connects different parts of the brain. Diffusion MRI
enables a range of tools that permit qualitative and quantitative assessments of many
neurological disorders [3].
Diffusion magnetic resonance imaging

Flow chart illustrating the processing pipeline [12]

Tractography
● Tractography is a collection of methods
used to reconstruct white matter
pathways in the human brain, using the
orientation information derived from the
used diffusion model.

● The diffusion tensor's directional

anisotropic information offers a singular
opportunity for noninvasively estimating
and modeling the trajectories of white
matter tracts in the human brain.

MRI of the brain and automated whole

brain tractography [6]
Tractography

● White matter tractography is the name given to the algorithms used to map
these connectivity patterns [7].

● The main steps in the tractography: the first is to fit a diffusion model at each
voxel of the image, and the second is fiber tracking across voxels [8].

● The extraction of tracts is done using tractography algorithms which are

categorized into two classes, deterministic and probabilistic tractography [5]
Deterministic algorithms
● Deterministic methods tend to be simple and fast
● Linear propagation approach, called FACT (Fiber Assignment by Continuous
Tracking), is considered as the first published tractography technique
● Deterministic algorithms follow the main fiber directions as revealed by the
diffusion model and generate sequences of points that are considered as
fibers.
● Deterministic tractography algorithms perform tracking of streamlines by
following a predictable path, such as following the primary diffusion direction
[10].
● Many Deterministic algorithms are reported in literature :
Deterministic algorithms

● HARDI-based techniques include the generalization of streamline tracking to

use ODFs (Orientation diffusion function) computed from diffusion spectrum
imaging.
● Multi-tensor tracking
● Q-ball tracking
● ODF tracking

Schematic illustration of the tractography analysis [12]

Probabilistic algorithms
● Probabilistic
using methods
information for determining
obtained the MRI
from diffusion connectivity between brain regions
● Probabilistic algorithms repeat the deterministic version many times by
randomly perturbing the main fiber directions each time, and produce maps of
connectivity
● Such maps indicate the probability that a given voxel is connected to a
reference position. [11].
Probabilistic algorithms : Monte Carlo Method
● Given
attempt
that probability
points
to compute
A and
is given
Bthe
in as
probability
a diffusion
[13] : ofMRI,
a tract
probabilistic
connectingtractography
A and B. Formally,
algorithms

● Theorientation
probabilistic
generated.
the PIC (probabilistic
The
fibre
PDFs
method
tracking
within
index
utilises
allowing
each
of connectivity)
a voxel
Monte
mapson
Carlo
ofeach
connection
framework
streamline
iterationprobability
is[14].
approach,
used to enable
to sampling
be
Probabilistic Algorithms : Monte Carlo Method
●
● Utilising
defined
describe
Each PDFprobability
at
information
acquisition each
the
orientation. is
inlocal density
point
intended
available
terms ofwithin
uncertainty
to
from
the afunctions
thein brain
interpret fibre
the
diffusion
likely (PDFs)
to
imaging
underlying
● fibre
Given
be
scale,
brain.structure.
an
possible
anatomical accurate
between
This to
may any
be voxelwise
define
connection, the
two defined
points
achieved
Carlo approaches based on, for PDF
probabilityat
within
using it
theshould
of voxel
the
Monte

[14]
Tractogram filtering

● Tractography is prone to find false-positive streamlines causing a severe decline in its specificity and limiting its
feasibility in accurate structural brain connectivity analyses.
● Filtering algorithms have been proposed to reduce the number of invalid streamlines but the currently available
filtering algorithms are not suitable to process data that contains motion artefacts which are typical in clinical
research.
● Augmented the Convex Optimization Modelling for Microstructure Informed Tractography (COMMIT) algorithm to
adjust for these signals drop-out motion artefacts.
● It was demonstrate with comprehensive Monte-Carlo whole brain simulations and in vivo infant data that our robust
algorithm is capable of properly filtering tractography reconstructions despite these artefacts.
● Usage of robust filtering methods to mitigate motion related errors in tractogram filtering is highly beneficial,
especially in clinical studies with uncooperative patient groups such as infants. With our presented robust
augmentation and open-source implementation, robust tractogram filtering is readily available [4].
● Diffusion tensor imaging (DTI) is a modality known to be highly sensitive to the detrimental effects of
experimental noise. Monte Carlo method can be used to improve signal-to-noise ratio (SNR) [14,15].
Brain network analysis for diagnostic
● cognitive disorders.
Tractography can reveal brain abnormalities in multiple sclerosis a variety of
● Network analysis
properties of brainofnetworks
these brain
helpconnectivity
identify disease-related
matrices candifferences
reveal organizational
[13].
● Tractography has become an indispensable tool for studies on various brain
disorders.
Programs
● TALON: Tractograms As Linear Operators in Neuroimaging
● WL-align
● COMMIT
● PyUNLocBoX: Optimization by Proximal Splitting
programs
● Dmipy: Diffusion Microstructure Imaging in PyMrtrix3

● Brain Connectivity Toolbox

● ANIMA

● BrainSUITE

● SlicerDMRI

● Dipy
References
[1] Xavier, G., (2009). Global Brain Connectivity Analysis by Diffusion MR Tractography: Algorithms, Validation and Applications.

[2] Zhang, F., Daducci, A., He, Y., Schiavi, S., Seguin, C., Smith, R. E., Yeh, C. H., Zhao, T., & O’Donnell, L. J. (2022). Quantitative mapping of the brain’s structural
connectivity using diffusion MRI tractography: A review. NeuroImage, 249, 118870. https://doi.org/10.1016/j.neuroimage.2021.118870

[3] Xuan, G., (2017). Advanced analysis of diffusion MRI data.

[4] Sairanen, V., Ocampo-Pineda, M., Granziera, C., Schiavi, S., & Daducci, A. (2022). Incorporating outlier information into diffusion-weighted MRI modeling for robust
microstructural imaging and structural brain connectivity analyses. NeuroImage, 247, 118802. https://doi.org/10.1016/j.neuroimage.2021.118802

[5] Aronis, C., Delibasis, K., Fanariotis, M., & Maglogiannis, I. (2016). A Tractography Algorithm for MR Diffusion Tensor Imaging Based on Minimum-Cost Path. XIV
Mediterranean Conference on Medical and Biological Engineering and Computing 2016, 302–307. https://doi.org/10.1007/978-3-319-32703-7_60

[6] Zakaria, H., Haider, S., & Lee, I. (2017). Automated Whole Brain Tractography Affects Preoperative Surgical Decision Making. Cureus. https://doi.org/10.7759/cureus.1656

[7] Alexander, A. L. (2010). Deterministic White Matter Tractography. Diffusion MRI, 383–395. https://doi.org/10.1093/med/9780195369779.003.0022

[8] Zhan, L., Zhou, J., Wang, Y., Jin, Y., Jahanshad, N., Prasad, G., Nir, T. M., Leonardo, C. D., Ye, J., Thompson, P. M., & for the Alzheimer’s Disease Neuroimaging Initiative.
(2015). Comparison of nine tractography algorithms for detecting abnormal structural brain networks in Alzheimer’s disease. Frontiers in Aging Neuroscience, 7.
https://doi.org/10.3389/fnagi.2015.00048
References
[9] S. Mori, B. J. Crain, V. P. Chacko, and P. C. van Zijl. Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging. Ann Neurol, 45:265–269, 1999.

[10] Deterministic tractography – Introduction to dMRI. (n.d.). The Carpentries Incubator - Introduction to dMRI. https://carpentries-incubator.github.io/SDC-BIDS-dMRI/deterministic_tractography/index.html

[11] Fillard, P., Descoteaux, M., Goh, A., Gouttard, S., Jeurissen, B., Malcolm, J., Ramirez-Manzanares, A., Reisert, M., Sakaie, K., Tensaouti, F., Yo, T., Mangin, J. F., & Poupon, C. (2011). Quantitative
evaluation of 10 tractography algorithms on a realistic diffusion MR phantom. NeuroImage, 56(1), 220–234. https://doi.org/10.1016/j.neuroimage.2011.01.032

[12] Petersen, M. V., Lund, T. E., Sunde, N., Frandsen, J., Rosendal, F., Juul, N., & Østergaard, K. (2017). Probabilistic versus deterministic tractography for delineation of the cortico-subthalamic hyperdirect
pathway in patients with Parkinson disease selected for deep brain stimulation. Journal of Neurosurgery, 126(5), 1657–1668. https://doi.org/10.3171/2016.4.jns1624

[13] Zhan, L., Zhou, J., Wang, Y., Jin, Y., Jahanshad, N., Prasad, G., Nir, T. M., Leonardo, C. D., Ye, J., Thompson, P. M., & for the Alzheimer’s Disease Neuroimaging Initiative. (2015). Comparison of nine
tractography algorithms for detecting abnormal structural brain networks in Alzheimer’s disease. Frontiers in Aging Neuroscience, 7. https://doi.org/10.3389/fnagi.2015.00048

[14] Huang, H., Zhang, J., van Zijl, P. C., & Mori, S. (2004). Analysis of noise effects on DTI-based tractography using the brute-force and multi-ROI approach. Magnetic Resonance in Medicine, 52(3),
559–565. https://doi.org/10.1002/mrm.20147

[15] Bastin, M. E., Armitage, P. A., & Marshall, I. (1998). A theoretical study of the effect of experimental noise on the measurement of anisotropy in diffusion imaging. Magnetic Resonance Imaging, 16(7),
773–785. https://doi.org/10.1016/s0730-725x(98)00098-8