from Australia Connectomes course 2018 in Melbourne, Australia. A brief introduction to CPAC and an in depth lecture on how to preprocessing functional MRI data.
This presentation introduces medical professionals and allied healthcare associates to the fundamental rationale, objectives, techniques, and utilizations of intraoperative neurophysiologic monitoring (IONM).
These are slides for an introductory lecture on fMRI/MRI and analysis of fMRI data. The corresponding tutorial is available on my website kathiseidlrathkopf.com
Local Field Potential (LFP): Literature ReviewMd Kafiul Islam
Local Field Potential (LFP), recorded from invasive (in-vivo) neural recordings either by surface of cortex (ECoG/iEEG) or from inside the cortex, has gained increased attention alongside with neural spikes for understanding the information processing of brain and thus relating brain dynamics to a particular behavior or disease. The complete understanding of the underlying mechanism of LFP is yet to be discovered, but it's of no doubt that LFP would be the future to understand our brain in a better way.
This presentation introduces medical professionals and allied healthcare associates to the fundamental rationale, objectives, techniques, and utilizations of intraoperative neurophysiologic monitoring (IONM).
These are slides for an introductory lecture on fMRI/MRI and analysis of fMRI data. The corresponding tutorial is available on my website kathiseidlrathkopf.com
Local Field Potential (LFP): Literature ReviewMd Kafiul Islam
Local Field Potential (LFP), recorded from invasive (in-vivo) neural recordings either by surface of cortex (ECoG/iEEG) or from inside the cortex, has gained increased attention alongside with neural spikes for understanding the information processing of brain and thus relating brain dynamics to a particular behavior or disease. The complete understanding of the underlying mechanism of LFP is yet to be discovered, but it's of no doubt that LFP would be the future to understand our brain in a better way.
Estimating the hemodynamic response function from resting state fMRI datadanielemarinazzo
These slides describe the methodology that we developed to estimate the hemodynamic response function (HRF) from resting state fMRI scans.
Additionally, some applications are presented.
A simple introduction to fMRI study design for social science and other researchers outside the field who might want to design a study using fMRI brain scanning technology
Open science resources for `Big Data' Analyses of the human connectomeCameron Craddock
Neuroimaging has become a `Big Data' pursuit that requires very large datasets and high throughput computational tools. In this talk I will highlight many open science resources for acquiring the necessary data. This is from a lecture that I gave in 2015 at the USC Neuroimaging and Informatics Institute.
MRI biomarkers for the spinal cord, webinar with Dr. Julien Cohen-Adad.jcohenadad
The video recording is available here: 👉 https://youtu.be/3_xJCSqu5xs
Neuroimaging MRI biomarkers include volumetric measures, microstructure imaging such as diffusion-weighted imaging and magnetization transfer, and functional MRI. These biomarkers nicely complement clinical indices and provide objective means to monitor disease evolution in patients. While being very popular in the brain, MRI biomarkers have been slow to translate to the spinal cord because of the technical difficulties in imaging this organ. In this talk, I will present state-of-the-art solutions for the acquisition and automatic analysis of MRI biomarkers in the spinal cord. During the first part of the talk, I will talk about a recent initiative to standardize acquisition protocol in the spinal cord: the spine-generic project (https://spine-generic.rtfd.io/). During the second part of the talk, we will go through some of the main features of the Spinal Cord Toolbox (SCT, http://spinalcordtoolbox.com/), a popular open-source software package which performs automatic analysis of spinal cord MRI biomarkers.
Finally, we will show example applications of these advanced acquisition and processing methods in various multi-center studies and applied to a variety of diseases: multiple sclerosis, amyotrophic lateral sclerosis, degenerative cervical myelopathy, chronic pain and cancer.
Dr. Cohen-Adad is an Associate Professor at Polytechnique Montreal, Adjunct Professor in the Department of Neurosciences at University of Montreal, Associate Director of the Neuroimaging Functional Unit at the University of Montreal, and Canada Research Chair in Quantitative Magnetic Resonance Imaging. His research focuses on advancing hardware and software MRI methods to help characterizing pathologies in the central nervous system, with a particular focus in the spinal cord. He has published over 130 articles on that topic (https://scholar.google.ca/). Dr. Cohen-Adad also dedicates efforts in bringing the community together by developing open source solutions and by organizing yearly workshops via the www.spinalcordmri.org platform, which he initiated.
Links to publications and work of Dr. Julien Cohen-Adad:
https://pubmed.ncbi.nlm.nih.gov/33039...
https://pubmed.ncbi.nlm.nih.gov/32572...
https://scholar.google.ca/citations?u...
https://spine-generic.rtfd.io/
Estimating the hemodynamic response function from resting state fMRI datadanielemarinazzo
These slides describe the methodology that we developed to estimate the hemodynamic response function (HRF) from resting state fMRI scans.
Additionally, some applications are presented.
A simple introduction to fMRI study design for social science and other researchers outside the field who might want to design a study using fMRI brain scanning technology
Open science resources for `Big Data' Analyses of the human connectomeCameron Craddock
Neuroimaging has become a `Big Data' pursuit that requires very large datasets and high throughput computational tools. In this talk I will highlight many open science resources for acquiring the necessary data. This is from a lecture that I gave in 2015 at the USC Neuroimaging and Informatics Institute.
MRI biomarkers for the spinal cord, webinar with Dr. Julien Cohen-Adad.jcohenadad
The video recording is available here: 👉 https://youtu.be/3_xJCSqu5xs
Neuroimaging MRI biomarkers include volumetric measures, microstructure imaging such as diffusion-weighted imaging and magnetization transfer, and functional MRI. These biomarkers nicely complement clinical indices and provide objective means to monitor disease evolution in patients. While being very popular in the brain, MRI biomarkers have been slow to translate to the spinal cord because of the technical difficulties in imaging this organ. In this talk, I will present state-of-the-art solutions for the acquisition and automatic analysis of MRI biomarkers in the spinal cord. During the first part of the talk, I will talk about a recent initiative to standardize acquisition protocol in the spinal cord: the spine-generic project (https://spine-generic.rtfd.io/). During the second part of the talk, we will go through some of the main features of the Spinal Cord Toolbox (SCT, http://spinalcordtoolbox.com/), a popular open-source software package which performs automatic analysis of spinal cord MRI biomarkers.
Finally, we will show example applications of these advanced acquisition and processing methods in various multi-center studies and applied to a variety of diseases: multiple sclerosis, amyotrophic lateral sclerosis, degenerative cervical myelopathy, chronic pain and cancer.
Dr. Cohen-Adad is an Associate Professor at Polytechnique Montreal, Adjunct Professor in the Department of Neurosciences at University of Montreal, Associate Director of the Neuroimaging Functional Unit at the University of Montreal, and Canada Research Chair in Quantitative Magnetic Resonance Imaging. His research focuses on advancing hardware and software MRI methods to help characterizing pathologies in the central nervous system, with a particular focus in the spinal cord. He has published over 130 articles on that topic (https://scholar.google.ca/). Dr. Cohen-Adad also dedicates efforts in bringing the community together by developing open source solutions and by organizing yearly workshops via the www.spinalcordmri.org platform, which he initiated.
Links to publications and work of Dr. Julien Cohen-Adad:
https://pubmed.ncbi.nlm.nih.gov/33039...
https://pubmed.ncbi.nlm.nih.gov/32572...
https://scholar.google.ca/citations?u...
https://spine-generic.rtfd.io/
Computational approaches for mapping the human connectomeCameron Craddock
Describes open challenges and ongoing work for mapping the human functional connectome and identifying inter-individual variation in the connectome that maps to phenotype and clinical outcomes. Also describes open science initiatives to help scientists from disparate backgrounds to become involved in this research.
In this paper we present the use of a signal processing technique to find dominant channels in
near infrared spectroscopy (NIRS). Cross correlation is computed to compare measuring
channels and identify delays among the channels. In addition, visual inspection was used to
detect potential dominant channels. The results showed that the visual analysis exposed painrelated
activations in the primary somatosensory cortex (S1) after stimulation which is
consistent with similar studies and the cross correlation analysis found dominant channels on
both cerebral hemispheres. The analysis also showed a relationship between dominant channels
and neighbouring channels. Therefore, our results present a new method to detect dominant
regions in the cerebral cortex using near-infrared spectroscopy. These results have also
implications in the reduction of number of channels by eliminating irrelevant channels for the
experiment.
CROSS CORRELATION ANALYSIS OF MULTI-CHANNEL NEAR INFRARED SPECTROSCOPYcscpconf
In this paper we present the use of a signal processing technique to find dominant channels in near infrared spectroscopy (NIRS). Cross correlation is computed to compare measuring channels and identify delays among the channels. In addition, visual inspection was used to detect potential dominant channels. The results showed that the visual analysis exposed painrelated activations in the primary somatosensory cortex (S1) after stimulation which is consistent with similar studies and the cross correlation analysis found dominant channels on both cerebral hemispheres. The analysis also showed a relationship between dominant channels
and neighbouring channels. Therefore, our results present a new method to detect dominant regions in the cerebral cortex using near-infrared spectroscopy. These results have also implications in the reduction of number of channels by eliminating irrelevant channels for the experiment.
CROSS CORRELATION ANALYSIS OF MULTI-CHANNEL NEAR INFRARED SPECTROSCOPYcscpconf
In this paper we present the use of a signal processing technique to find dominant channels in near infrared spectroscopy (NIRS). Cross correlation is computed to compare measuring channels and identify delays among the channels. In addition, visual inspection was used to detect potential dominant channels. The results showed that the visual analysis exposed painrelated activations in the primary somatosensory cortex (S1) after stimulation which is consistent with similar studies and the cross correlation analysis found dominant channels on both cerebral hemispheres. The analysis also showed a relationship between dominant channels and neighbouring channels. Therefore, our results present a new method to detect dominant regions in the cerebral cortex using near-infrared spectroscopy. These results have also implications in the reduction of number of channels by eliminating irrelevant channels for the experiment
Genetics influence inter-subject Brain State Prediction.Cameron Craddock
Poster from 2011 Annual Meeting of the Organization for Human Brain Mapping.
Support vector regression trained to predict intrinsic brain activity from one individual, applied to their twin, works better for identical twins than fraternal twins.
Talk from OHBM education day 2018, an overview of data sharing and other resources for neuroimaging research. Also a brief discussion of the impact that openly shared data has had on publications.
Prediction Analysis in Clinical and Basic NeuroscienceCameron Craddock
Talk given at the Resting State and Brain Connectivity 2016 conference symposium "The Emerging Field of Predictive Analytics in Neuroimaging: Applications, Challenges and Perspectives"
Using RealTime fMRI Based Neurofeedback To Probe Default Network RegulationCameron Craddock
Talk given at the 63rd Annual Meeting of the American Academy of Child & Adolescent Psychiatry. Describes an experiment using realtime fMRI neurofeedback to probe participants ability to modulate default network regulation along with preliminary results.
Using RealTime fMRI Based Neurofeedback to Probe Default Network RegulationCameron Craddock
Seminar given at the University of Illinois at Chicago Behavioral Neuroscience Seminar Series. The Default Network (DN) is a set of brain regions that are deactivated during the performance of externally triggered goal-drive tasks and active during spontaneous cognition. Activation of the DN during times when it should be off, has been hypothesized to be a symptom of several mental health disorders such as ADHD, depression, and anxiety. We describe the use of real-time fMRI to probe DN function in patient populations and children.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
3. The Human Connectome
• The sum total of all of the brain’s
connections
– Structural connections: synapses and
fibers
• Diffusion MRI
– Functional connections: synchronized
physiological activity
• Resting state functional MRI
• Nodes are brain areas
• Edges are connections
Craddock et al. Nature Methods, 2013.
5. Resting State Functional Connectivity
Biswal et al. MRM 1995
Intrinsic activity is ‘‘ongoing neural and metabolic
activity which is not directly associated with
subjects’ performance of a task’’-Raichle TICS 2010
7. Configurable Pipeline for the Analysis of
Connectomes (CPAC)
• Pipeline to automate preprocessing and analysis
of large-scale datasets
• Most cutting edge functional connectivity
preprocessing and analysis algorithms
• Configurable to enable “plurality” – evaluate
different processing parameters and strategies
• Automatically identifies and takes advantage of
parallelism on multi-threaded, multi-core, and
cluster architectures
• “Warm restarts” – only re-compute what has
changed
• Open science – open source
• http://fcp-indi.github.io
Nypipe
8. Forking Example
Raw EPI
Slice time correction
Motion realignment
Friston 24-Parameter
model
Calculate motion
statistics
Calculate mean EPI
Calculate EPI mask
Apply mask to
mean EPI
Apply mask to
realigned EPI
Raw anatomical
Reorient, de-oblique,
and skull-strip
Calculate anatomical
to MNI registration
Anatomical
segmentation
Calculate EPI to
anatomical registration
using BB-reg
Nuisance correction
Warp motion and
nuisnace-corrected EPI to MNI
Band-pass filt er
Warp fil
t
ered , motion
and nuisnace-corrected EPI to MNI
Centrality mask
Calculate network
centrality (no filt er)
Smooth centrality
output (no filt er)
Calculate network
centrality (filt ered)
Smooth centrality
output (filt ered)
12. No consensus on preprocessing
Non-white noise in fMRI: Does modelling have an impact?
Torben E. Lund,a,* Kristoffer H. Madsen,a,b
Karam Sidaros,a
Wen-Lin Luo,c
and Thomas E. Nicholsd
a
Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital, Hvidoure, Kettegaard Alle´ 30, 2650 Hvidovre, Denmark
b
Informatics and Mathematical Modelling, Technical University of Denmark, Lyngby, Denmark
c
Merck & Co., Inc., Whitehouse Station, New Jersey 08889-0100, USA
d
Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109-2029, USA
Received 16 December 2004; revised 1 July 2005; accepted 6 July 2005
Available online 11 August 2005
The sources of non-white noise in Blood Oxygenation Level Dependent
(BOLD) functional magnetic resonance imaging (fMRI) are many.
Familiar sources include low-frequency drift due to hardware
imperfections, oscillatory noisedueto respiration and cardiac pulsation
and residual movement artefacts not accounted for by rigid body
registration. These contributions give rise to temporal autocorrelation
in theresidualsof thefMRI signal and invalidate thestatistical analysis
as the errors are no longer independent. The low-frequency drift is
often removed by high-pass filtering, and other effects are typically
modelled as an autoregressive (AR) process. In this paper, we propose
an alternative approach: Nuisance Variable Regression (NVR). By
identically normally distributed (i.i.d.), thisobservation isimportant
and hashad largeimpact on paradigm design and dataanalyses.
With non-white noise, the i.i.d. assumption is no longer
fulfilled, and if this is ignored, the estimated standard deviations
will typically be negatively biased, resulting in invalid (liberal)
statistical inferences. Another consequence is the difficulty in
detecting signals when covered in noise. As we are normally
interested in the GM signal, it is problematic that this is the region
where structured noise is most pronounced. With physiological
noise increasing with field strength (Kru¨ger and Glover, 2001;
www.elsevier.com/locate/ynimg
NeuroImage 29 (2006) 54 – 66
e noise in fMRI: Does modelling have an impact?
nd,a,* Kristoffer H. Madsen,a,b
Karam Sidaros,a
c
and Thomas E. Nicholsd
tre for Magnetic Resonance, Copenhagen University Hospital, Hvidoure, Kettegaard Alle´ 30, 2650 Hvidovre, Denmark
ematical Modelling, Technical University of Denmark, Lyngby, Denmark
hitehouse Station, New Jersey 08889-0100, USA
istics, University of Michigan, Ann Arbor, Michigan 48109-2029, USA
r 2004; revised 1 July 2005; accepted 6 July 2005
ugust 2005
hite noisein Blood Oxygenation Level Dependent
magnetic resonance imaging (fMRI) are many.
clude low-frequency drift due to hardware
identically normally distributed (i.i.d.), thisobservation isimportant
andhashadlargeimpact onparadigmdesignanddataanalyses.
www.elsevier.com/locate/ynimg
NeuroImage 29 (2006) 54 – 66
A component based noise correction method (CompCor) for BOLD
and perfusion based fMRI
Yashar Behzadi,a,b
Khaled Restom,a
Joy Liau,a,b
and Thomas T. Liua,⁎
a
UCSD Center for Functional Magnetic Resonance Imaging and Department of Radiology, 9500 Gilman Drive, MC 0677, La Jolla, CA 92093-0677, USA
b
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
Received 18 December 2006; revised 23 April 2007; accepted 25 April 2007
Available online 3 May 2007
A component based method (CompCor) for the reduction of noise in
both blood oxygenation level-dependent (BOLD) and perfusion-
based functional magnetic resonance imaging (fMRI) data is
presented. In the proposed method, significant principal components
are derived from noise regions-of-inter est (ROI) in which the time
series data are unlikely to be modulated by neural activity. These
components are then included as nuisance parameters within general
linear models for BOLD and perfusion-based fMRI time series data.
Two approaches for the determination of the noise ROI are
neurovascular coupling mechanisms (Hoge et al., 1999). However,
as the fMRI community has moved to higher field strengths,
physiological noise has become an increasingly important
confound limiting the sensitivity and the application of fMRI
studies (Kruger and Glover, 2001; Liu et al., 2006).
Physiological fluctuations have been shown to be a significant
source of noise in BOLD fMRI experiments, with an even greater
effect in perfusion-based fMRI utilizing arterial spin labeling
www.elsevier.com/locate/ynimg
NeuroImage 37 (2007) 90– 101
This is particularly complicated for “post-hoc” aggregated datasets
13. Anatomical Processing
• Information from
structural MRI images
are required for:
– Warping images into a
common space
– Calculating tissue maps
for data cleaning
operations
15. Skullstripping
• Remove “non-brain” tissue from
the image that may interfere with
spatial normalization and
segmentation
– When skull-stripping is good, it can
substantially improve the quality of
alignment
– When it is bad, it will substantially
degrade the quality of alignment to
worse that what is obtainable with
skull-on
– No “silver bullet” that seems to
work robustly for all datasets
16. Spatial Normalization
• Quality of alignment
between resultant images
are determined by:
– Algorithm
– Quality of the template
– Initial starting orientation
of the individual images
17. Optimizing Spatial Normalization
• Choose a template based on
your population – there are
a variety of templates for
different age groups
• Consider a lower resolution
template to reduce
processing time and
memory requirements
– 2mm for fMRI
– 1mm for VBM
fNIRT ANTs
DPARSF 3dQWarp
18. Segmentation
• Calculate tissue specific masks for sMRI – fMRI
co-registration and extracting nuisance
regressors (WM and CSF) for denoising
19. Functional Preprocessing
1. Distortion correction
2. Drop first N TRs
3. Slice timing correction
4. Motion coregistration
5. Calculate EPI-T1 transform
6. Nuisance Variable Regression
7. Bandpass filter
8. Calculate derivative (fc map)
9. Copy into template space
10. Spatial Smoothing
20. Distortion Correction
• Echo-planar imaging can produce
large geometric image distortions
near areas of high magnetic
susceptibility (air/tissue interfaces)
• This can be mathematically corrected
using information from field maps
and blip up/down acquisitions
• In practice results are fairly subtle
https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/reg.pdf
21. Discarding the first few scans
• First few TRs have different
signal profile than the
remainder
• This may have been
automatically discarded by
the scanner, if not discard
before analysis
• The number of frames to
discard is determined by the
flip angle
22. Slice Timing Correction
• Slices of an fMRI volume are
acquired at different times,
resulting in delays between BOLD
time courses from different parts
of the brain
• Corrected by interpolating time
points to the same sampling grid
• Interacts with head motion
correction
• May not be needed for low-TR
sequences or if bandpass filtering
23. Motion Co-registration
• Motion that occurs
between the acquisitions of
fMRI volumes can be
corrected by co-registration
• Motion that occurs
between slices in an volume
cannot be accounted for so
easily
– Maybe drop the frames and
replaces with interpolation??
24. Motion induced intensity modulations
• Head motion also induces
variations in the fMRI signal
– Spin-history effects
– Partial voluming
• Can be excluded by scrubbing
(deleting volumes and
interpolating) motion peaks
• Or including head motion in
the nuisance regression
(discussed later)
25. EPI – T1 Transform
• To calculate an EPI – MNI space transform,
the data are first co-registered to the T1
and the resulting transform is combined
with the T1-MNI transform
• Boundary based registration relies on
information from the white – grey matter
boundary for a better alignment
• Requires good WM segmentation
• Also requires good contrast in EPI
volumes, may make registration worse for
images with poor contrast (multiband
data?)
26. Nuisance Variable Regression
• fMRI signal is a combination of neuronal signal, cardiac
pulse, respiration, motion induced variations, scanner
drifts, and other noise sources
• Can fit a regression model to estimate the contributions of
the nuisance signals and subtract them out
• The quality of the denoising is dependent on the quality of
models of the various components
27. Cardiac and Respiration
• Cardiac pulsation induces
micro-movements in the brain
• Variations in abdominal
oxygen content due to
breathing causes variations in
the magnetic field that create
global intensity variations
• Long term changes in depth
and rate of breathing change
brain oxygenation level and
can effect BOLD response
28. Correcting for Physiological noise
• If you have recordings of pulse and respiration you can use
them to derive a model of their effects on the bold signal
(RETROICOR)
• Without these measurements, can use mean wm signal as
a surrogate for respiration and mean csf signal as a
surrogate for pulsation
– Need to be very careful not to include neuronal signal in these
regressors
• Can use CompCor or Anaticorr to account for regional
variation in the effects (i.e. due to multichannel head coils)
29. Models for head motion
• Various models have been proposed for motion
regressors
– 6 parameters from motion correction
– 12 parameters: 6 parameters and their one lags
– 24 parameters: 6 parameters, one lags, and the squares of
both of these
– “spike regression” to exclude specific volumes and replace
with interpolation
• Evidence is supporting the 24 parameter model
30. Global Signal Regression
• GSR helps “clean up” functional
connectivity, results in better
definition of networks
– shown to help address head motion
• GSR always induces negative
correlations
– Hard to interpret negative correlations,
not necessarily true ‘anti-correlations’ or
inhibition
• Global signal has interesting inter-
individual variation
Yan 2012
31. Bandpass filtering
• Bandpass filtering (0.01 < f < 0.1 Hz) is used to eliminate high frequency
variation not associated with resting state FC
• But due to aliasing, probably not perfectly effective
• Also, there is evidence that FC information also exists at higher
frequencies
33. Derivatives
• Seed-based correlation – multiple regression
• Time series extraction – eigen or mean, many atlases pre-loaded
• ALFF/fALFF
• Regional homogeneity
• Voxel-mirrored homotopic connectivity
• Network centrality (degree, eign, lfcd) – optimized for efficiency
• Dual regression
• Bootstrap analysis of stable clusters
• Group-level analyses (ANOVA/ANCOVA)
• Multivariate Distance Matrix Regression
34. Copy to MNI space and smooth
• To reduce the amount of “blob spread” due to spatial
smoothing, results are written into MNI space after
derivative calculation
– iFC, dual regression, ReHo, f/alff
• Other derivatives are calculated in MNI space
– Centrality, VMHC
• Smoothing is employed to improve SNR, correspondence
between individuals, and to make the data more consistent
with group-level modeling assumptions