Vancouver, June 25, 2017

Educational Course
Advanced methods for cleaning up fMRI time-series

How-to use ICA

for de-noising
Ludovica Griffanti
FMRIB Centre, University of Oxford, Oxford,
United Kingdom
 Overview
• Why ICA to clean fMRI?
• How to use ICA to clean fMRI?
• How to perform components classification?
• Characteristics of signal and noise: features

• Hands-on: signal or noise?

• Automated approaches
• Factors that impact IC characteristics
• Effect of ICA-based cleaning
 Why ICA to clean fMRI?
• Data-driven separation (no need of external
recordings or priors)
space components space
time

components
time
Scan #k
spatial maps
FMRI data =

components
 Why ICA to clean fMRI?
• Data-driven separation (no need of external
recordings or priors)
→ no info on which IC is signal
and which is noise

• Multiple noise classes (motion, physiological,

scanner-related)
→ no info on what sub-class of
noise it belongs to

• Subject-specific
→ heterogeneity of ICs across
subjects
How to use ICA to clean fMRI?
fMRI dataset (after basic preprocessing)

1) ICA algorithm

ICA-based de-noising
ICs (time series + spatial maps)

2) ICA classification
(manual, semi-automated,
automated)

Signal ICs Noise ICs

3a) non-aggressive 3b) aggressive

cleaning cleaning

Denoised fMRI dataset

 How to perform component
classification?
MANUAL:
“An expert manual classification of components as either artifact or unlikely
artifact was performed”

“…this is time consuming and highly subjective, and therefore automatic noise
component identification would be preferable…”

SEMI-AUTOMATED:
“…the training data consisted of independent component
pairs classified by an expert …”

AUTOMATED:
“…performance can be summarised by its accuracy … in
comparison with labels as provided by the experts…”
 Who is “the expert”?

• No absolute ground truth

• Very little description in literature about how to
classify components
• Need of a consensus rather than an expert

[Kelly et al., 2010; Griffanti et al., 2016a]

 Characteristics of signal and
noise: features
SPATIAL Features
Clusters # and dimension
Overlap with GM
Overlap with WM, CSF,
blood vessels
Overlap with brain
boundaries or areas close to follow known anatomical (e.g.
the edges of the FOV.
Location near area of
susceptibility induced signal
loss
Signal IC characteristic
Low number of large clusters
Clusters’ peaks in GM and
overall good overlap of the
clusters with GM, similarity with
common RSNs
Very low or absent overlap
Very low or absent overlap with
brain boundaries. Clusters
structural/ histological)
boundaries.
Generally located away from
these areas
Noise IC characteristic
Large number of small clusters
Indiscriminate overlap with non-
GM tissues, or clusters’ peaks in
WM/CSF
High overlap with one or more
Ring-like or crescent shape or
stripes near the edges of the field-
of-view
Located within the region of signal
loss (e.g. areas of air-tissue
interface)
 Characteristics of signal and
noise: features
TEMPORAL Features
Overall aspect of the time
series
Distribution of power in
frequency domain
Correlation with motion
regressors (realignment
parameters)
Correlation with task-related
regressors
Signal-IC characteristic Noise-IC characteristic
Fairly regular/oscillatory Large jumps and/or sudden change
time course of oscillation pattern.
Predominantly low
frequency (resting state: at
Predominantly high frequency, very
least one strong peak within
low frequency, or pan frequency
0.01 – 0.1 Hz), or frequency
of the stimulus (task)
Low correlation High correlation
High correlation Low correlation
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
 TOF image - courtesy of Tom Okell

http://simonrdownes.com/2014/05/ http://www.joeniekrofoundation.com/understanding/brain-basics/
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?
Hands-on: signal or noise?

More examples in: Griffanti et al., 2016a

 Recap: how to look at the
components?
• Underlay different modalities (highres T1, EPI)
• Change threshold (peaks, anatomy)
• Look at different planes
• Compare with realignment parameters (or task stimuli)
• Smooth data (or components, for visualisation only)

• Look at both positive and negative clusters

• Look at components in surface space
• Expect high proportion of noise components
 Recap: how to look at the
components?
• Set priorities:
1) spatial map, 2) time series, 3) power spectrum
• Main aim is to retain as much signal as possible:
“Innocent until proven guilty”
• No hard-rule or ground truth: multiple loops
• Be consistent and describe what you do
 Automated approaches
Any (automatic) help for IC classification?
• Good visualisation tool [FSLeyes “melodic view”, workbench, etc.]
• Quantify features to help classification
• Amount of overlap with GM/WM/CSF
• Fraction of power spectrum in different frequency bands
• Identification of outliers/spikes (DVARS, FD, etc.)
[Kelly et al., 2010; Allen et al., 2011; Cardinale et al., 2013; Vergara et al., 2016]

• IC-fingerprints [DeMartino et al., 2007]

 Automated approaches
Freely available tools
Training
Approach Purpose #features Classifier type
required?
SOCK multiple k-means clustering, 5
[Bhaganagarapu et l., sources of 4 combinations of NO
2013] noise conditions
FIX multiple Hierarchical fusion
[Salimi-Khorshidi et sources of >180 (kNN, decision tree, YES
al., 2014] noise SVM)
multiple
Sparse Logistic
Sochat et al., 2014 sources of 246 YES
Regression
noise

AROMA Noise if exceeds at

Motion 4 NO
[Pruim et al., 2015] least one of 3 criteria
Factors that impact ICs characteristics
Acquisition (data quality and type)
• Spatial and temporal resolution → # and quality of ICs
• Scanner/sequence specific artefacts → know your
acquisition parameters (MB factor, TR)
• Multi-echo
Preprocessing
• Smoothing
• Multi-stage cleaning
Population/condition
• Patients → specific alterations, more motion
• Task-based fMRI → task-specific components
 Effect of ICA-based cleaning
• Better group-ICA components

Feis et al., 2015

Smith et al., 2013

 Effect of ICA-based cleaning
• Better discrimination with study-specific training dataset
(patients+controls)

Study-specific training

Griffanti et al., 2016b

 Thank you
Ludovica Griffanti
ludovica.griffanti@ndcn.ox.ac.uk
@ludogriffanti

Gwenaëlle Douaud
Sean Fitzgibbon
Janine Bijsterbosh
Robert Westphal
Stefania Evangelisti
Davide Carone
Fidel Alfaro-Almagro
Christian F. Beckmann
Matthew F. Glasser
Stephen M. Smith
Eugene P. Duff

References • Kelly et al., 2010, J Neurosci Methods 189, 233-245.

• Griffanti et al., 2016a, Neuroimage (in press)
• Allen et al., 2011, Front Syst Neurosci 5, 2
• Bhaganagarapu et l., 2013, Front Hum Neurosci 7, 343.
• Cardinale et al., 2013, JAMA Psychiatry 70(9), 975-82.
• De Martino et al., 2007, Neuroimage 34, 177-194.
• Demertzi et al., 2014, Cortex 52, 35-46.
• Feis et al., 2015, Front Neurosci. 9, 395.
• Griffanti et al., 2016b, Neuroimage, 124(Pt A), 704-13.
• Pruim et al., 2015, Neuroimage 112, 267-277.
• Rodionov et al., 2007, Neuroimage 38, 488-500.
• Salimi-Khorshidi et al., 2014, Neuroimage 90, 449-468.
• Smith et al., 2013, Neuroimage, 80, 144-68.
• Sochat et al., 2014, PLoS One 9, e95493.
• Soddu et al., 2011, Funct Neurol 26, 37-43.
• Vergara et al., 2016, Neuroimage, 145(Pt B), 365-376
• Zerbi et al., 2015, Neuroimage 123, 11-21.