![Page 1: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/1.jpg)
Translational
Neuromodeling
Unit
Noise Models and Correction for fMRI
Lars Kasper
Nov 21th, 2017
MR-Technology and Methods Group & Translational Neuromodeling Unit
Institute for Biomedical Engineering
University of Zurich and ETH Zurich
- an Introduction to the PhysIO Toolbox
![Page 2: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/2.jpg)
The Goal of Noise Correction
Lars Kasper: fMRI Noise Models & Correction
Before After
Noise Modeling &
Correction
2017-11-21 2
![Page 3: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/3.jpg)
The Goal of Noise Correction
Lars Kasper: fMRI Noise Models & Correction
Before After
Noise Modeling &
Correction
2017-11-21 3
![Page 4: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/4.jpg)
Reminder: fMRI Data is noisy...
2017-11-21 4Lars Kasper: fMRI Noise Models & Correction
![Page 5: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/5.jpg)
fMRI Data is noisy...
2017-11-21 5Lars Kasper: fMRI Noise Models & Correction
Interest in fluctuations
only: Subtract the meanMotion
Thermal
noise
Physiological
Noise
BOLD
effect
![Page 6: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/6.jpg)
Previously…
How we ended 6 weeks
ago (after preprocessing)
After smoothing…
still some fluctuation
2017-11-21 6Lars Kasper: fMRI Noise Models & Correction
![Page 7: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/7.jpg)
Sources of Noise in fMRI
Lars Kasper: fMRI Noise Models & Correction
Acquisition Timing
Subject Motion
Anatomical Identity
Inter-subject variability
Thermal Noise
Physiological Noise
Spatial Preproc
Temporal Preproc
Noise Modeling
Spatial Preproc
Spatial Preproc
Spatial Preproc
Slice-Timing
Realignment
Co-registration
Segmentation
Smoothing
PhysIO Toolbox
2017-11-21 7
![Page 8: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/8.jpg)
Previously….(continued)
ResMS image (cf. GLM lecture)
Indicates where
model incomplete…
limits sensitivity…
Lars Kasper: fMRI Noise Models & Correction
𝜎2 =𝑌 − 𝑋𝛽 2
𝑁 − 𝑝F contrast
All effects
2017-11-21 8
![Page 9: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/9.jpg)
Outline – Noise Correction
MRI Time Series Recap and Noise Sources
Why de-noising? Structured Noise; Noise Pathways
Noise Correction Approaches
Target: Scanner Drift, Motion, Cardiac/Breathing Cycle
Method: Modeling VS Preprocessing
Input: fMRI Data VS Peripheral Measures
Prospects for Improving Group Statistics
Limitations
Degrees of Freedom; Task-related “noise”; Interoception
Lars Kasper: fMRI Noise Models & Correction2017-11-21 9
![Page 10: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/10.jpg)
Outline – Noise Correction
MRI Time Series Recap and Noise Sources
Why de-noising? Structured Noise; Noise Pathways
Noise Correction Approaches
Target: Scanner Drift, Motion, Cardiac/Breathing Cycle
Method: Modeling VS Preprocessing
Input: fMRI Data VS Peripheral Measures
Prospects for Improving Group Statistics
Limitations
Degrees of Freedom; Task-related “noise”; Interoception
Lars Kasper: fMRI Noise Models & Correction2017-11-21 10
![Page 11: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/11.jpg)
fMRI = Acquiring Movies
Lars Kasper: fMRI Noise Models & Correction
Run/Session:
Time Series of
Images…
scan 1 time scan N
The Localized Time-series is
the Fundamental Information
Unit of fMRI
Signal: Fluctuation through
Blood oxygen level dependent
(BOLD) contrast
Noise: All other fluctuations
2017-11-21 11
![Page 12: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/12.jpg)
Noise Categories & Reduction
Lars Kasper: fMRI Noise Models & Correction
Noise: All other fluctuations
Thermal Noise
temporally uncorrelated
reduced SNR risk of
false negatives
Remedy: Spatial Smoothing
“Structured” Noise
temporally correlated
reduced SNR risk of false negatives
correlated with task risk of false positives
Remedy: Noise modeling (e.g. GLM)
Inference = Signal-To-Noise
2017-11-21 12
![Page 13: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/13.jpg)
Recap: MR Image Encoding
Lars Kasper: fMRI Noise Models & Correction2017-11-21 13
![Page 14: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/14.jpg)
Image Reconstruction & Noise
Lars Kasper: fMRI Noise Models & Correction
s =E m η+�
CoilSignal
EncodingMatrix
ObjectMagnetizatio
n
ThermalNoise
s1 =E1 m1 η1+�
s2 =E2 m2 η2+�
sN=EN mN ηN+�TimeSeries
ෝ𝑚 = 𝐸𝐻𝐸−1𝐸𝐻𝑠
Image reconstruction is also a
huge GLM, ~105-106 rows
3 mm slice, 8 chan: 642*8 = 512k
1 mm slice, 32 ch: 2562*32 = 2M
Any change between volumes
in encoding matrix (field),
object magnetization and
thermally induces image noise
s =E m η+�
CoilSignal
EncodingMatrix
ObjectMagnetizatio
n
ThermalNoise
s1 =E1 m1 η1+�
s2 =E2 m2 η2+�
sN=EN mN ηN+�TimeSeries
s =E m η+�
CoilSignal
EncodingMatrix
ObjectMagnetizatio
n
ThermalNoise
s1 =E1 m1 η1+�
s2 =E2 m2 η2+�
sN=EN mN ηN+�TimeSeries
2017-11-21 14
![Page 15: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/15.jpg)
What fluctuates?
Lars Kasper: fMRI Noise Models & Correction
ImagedObject MRSystemNoiseSources
EntryPointsofNoise
ForwardModel:MRImageEncoding
ReceiverChannels(ThermalNoise)
MagnetizationEncoding
MagneticFields
s =E m η+�s =E m η+�
CoilSignal
EncodingMatrix
ObjectMagnetizatio
n
ThermalNoise
s1 =E1 m1 η1+�
s2 =E2 m2 η2+�
sN=EN mN ηN+�TimeSeries
s =E m η+�
CoilSignal
EncodingMatrix
ObjectMagnetizatio
n
ThermalNoise
s1 =E1 m1 η1+�
s2 =E2 m2 η2+�
sN=EN mN ηN+�TimeSeries
2017-11-21 15
![Page 16: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/16.jpg)
Structured Noise in MRI
Lars Kasper: fMRI Noise Models & Correction
Magnetization
Cardiac
Cycle
Breathing
Cycle
Noise
Generator
Entry
Points of
Noise
Mediating
Mechanism
CSF
Flow
Head
Motion
Tissue
Pulsation
Blood
Flow/Vol
Arterial
CO2
Lung
Volume
Rigid Body
Displacement
Intra-Voxel
Composition
Inter-Voxel
Displacement
Heating
(“Drift”)
Magnet/Gradient
Deformation
Imaged
Object
MR Scanner
SystemNoise
Sources
Encoding
Magnetic
Fields
E m η+s =2017-11-21 16
![Page 17: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/17.jpg)
The Problem: Physiological Noise
Lars Kasper: fMRI Noise Models & Correction
Cardiac effects Respiratory effects
2017-11-21 17
![Page 18: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/18.jpg)
The Problem: Physiological Noise
Lars Kasper: fMRI Noise Models & Correction
Cardiac effects
Systole:
Blood pumped into brain, vessel
volume increases: pulsatile vessels
CSF pushed down: pulsatile CSF
Diastole:
Vessel volume decreases
CSF flows back into “void” brain
volume
A Cardiac Cycle in the Brain
2017-11-21 18
![Page 19: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/19.jpg)
The Problem: Physiological Noise
Lars Kasper: fMRI Noise Models & Correction
A Cardiac Cycle in the BrainTriggered High-Resolution fMRI
2017-11-21 19
![Page 20: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/20.jpg)
The Problem: Physiological Noise
Lars Kasper: fMRI Noise Models & Correction
Cardiac effects
Vessel Anatomy
Locations of
Fluctuations
2017-11-21 20
![Page 21: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/21.jpg)
The Problem: Physiological Noise
Lars Kasper: fMRI Noise Models & Correction
Cardiac effects Respiratory effects
Chest (&head) moves with
respiratory cycle
Changes in lung volume change
encoding magnetic field for MR
Geometric distortion/scaling
Respiratory-sinus arrythmia
Heart beats faster during inhalation
2017-11-21 21
![Page 22: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/22.jpg)
Outline – Noise Correction
MRI Time Series Recap and Noise Sources
Why de-noising? Structured Noise; Noise Pathways
Noise Correction Approaches
Target: Scanner Drift, Motion, Cardiac/Breathing Cycle
Method: Modeling VS Preprocessing
Input: fMRI Data VS Peripheral Measures
Prospects for Improving Group Statistics
Limitations
Degrees of Freedom; Task-related “noise”; Interoception
Lars Kasper: fMRI Noise Models & Correction2017-11-21 22
![Page 23: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/23.jpg)
Noise Correction Targets
Lars Kasper: fMRI Noise Models & Correction
Magnetization
Cardiac
Cycle
Breathing
Cycle
Noise
Generator
Entry
Points of
Noise
Mediating
Mechanism
CSF
Flow
Head
Motion
Tissue
Pulsation
Blood
Flow/Vol
Arterial
CO2
Lung
Volume
Rigid Body
Displacement
Intra-Voxel
Composition
Inter-Voxel
Displacement
Heating
(“Drift”)
Magnet/Gradient
Deformation
Imaged
Object
MR Scanner
SystemNoise
Sources
Encoding
Magnetic
Fields
E m η+s =2017-11-21 23
![Page 24: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/24.jpg)
Drifts: High-Pass Filtering
Discrete Cosine Model (last lecture) of slow
oscillations (cycle ≥ 128 s)
Was: Extra, non-task related columns in
design matrix: nuisance regressors
Now: Part of “hidden” preprocessing
Residual forming Matrix
𝐾 = 1 − 𝑋0 𝑋0𝑇𝑋0
−1𝑋0𝑇
With 𝑋0 being the design matrix modeling the confounds
In fact, GLM in SPM estimates
𝐾 ⋅ 𝒚 = 𝐾 ⋅ 𝑋 ⋅ 𝜷 + 𝐾 ⋅ 𝜀
2017-11-21 24Lars Kasper: fMRI Noise Models & Correction
𝑋0
![Page 25: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/25.jpg)
Modeling VS Preprocessing
Modeling:
Filters, projections (e.g. to independent components) etc. are all
linear operations
Combination in one design matrix, together with task
Simple test of correction efficacy: F-test on nuisance regressors
Preprocessing:
The data 𝑦 entering the GLM is altered ⇒ 𝑦′= 𝑋𝛽 + 𝜀
For non-linear changes of 𝑦 or inter-voxel dependencies,
alteration outside GLM necessary
Lars Kasper: fMRI Noise Models & Correction2017-11-21 25
![Page 26: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/26.jpg)
The Problem with Preprocessing
Problem: No inherent measure of efficacy (F-test in
GLM), correlation with task regressors undetected
“Advantage”: No loss of degrees of freedom
(sensitivity of F-test)
But it it only a hidden loss, statistics for inference is biased, if
performed modeling is not incorporated
Modeling via GLM recommended, if possible
Drifts, Motion Regressors
RETROICOR, HRV, RVT
aCompCor, (ICA)
2017-11-21 26Lars Kasper: fMRI Noise Models & Correction
![Page 27: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/27.jpg)
Motion: Preprocess & Modeling
Correction for motion artifacts is actually a combination of
Preprocessing and modeling
Preprocessing cannot correct spin-history effects, intra-
volume movements (non-rigid!), small partial volume effects
Preprocessing:
Realignment
Motion “Scrubbing”
Modeling (from estimated realignment parameters)
Retrospective Modeling: Motion Regressors
Motion Censoring
Lars Kasper: fMRI Noise Models & Correction2017-11-21 27
![Page 28: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/28.jpg)
Retrospective Motion Correction
Best: Avoid subject motion in the first place
Better: Use Prospective Motion Correction
Standard: Perform rigid-body realignment, use parameters
as nuisance regressors
6 parameters: translation+rotation
12 parameters: include derivatives (for temporal shifts)
24 parameters: include squared regressors
24-parameter model known as Volterra expansion
Lars Kasper: fMRI Noise Models & Correction
Friston, MRM,1996
2017-11-21 28
![Page 29: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/29.jpg)
Motion Censoring = “Scrubbing”
Detect outlier volumes (strong movement, but also
spikes, RF flip angle fluctuations)
Inform the GLM of these bad volumes via stick
regressors (zero everywhere else, 1 at volume)
Will absorb all variance of that volume
Problem: Temporal filtering before GLM might create
Gibbs ringing of outliers into neighbors
Alternative: censoring during preprocessing
interpolate faulty volume by neighbors
Lars Kasper: fMRI Noise Models & Correction
Power, NeuroImage, 2012
2017-11-21 29
![Page 30: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/30.jpg)
Noise Correction Targets
Lars Kasper: fMRI Noise Models & Correction
Magnetization
Cardiac
Cycle
Breathing
Cycle
Noise
Generator
Entry
Points of
Noise
Mediating
Mechanism
CSF
Flow
Head
Motion
Tissue
Pulsation
Blood
Flow/Vol
Arterial
CO2
Lung
Volume
Rigid Body
Displacement
Intra-Voxel
Composition
Inter-Voxel
Displacement
Heating
(“Drift”)
Magnet/Gradient
Deformation
Imaged
Object
MR Scanner
SystemNoise
Sources
Encoding
Magnetic
Fields
E m η+s =2017-11-21 30
![Page 31: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/31.jpg)
Image-based Noise Correction
Lars Kasper: fMRI Noise Models & Correction
PhysIO Toolbox
Exploratory
SpatialICA(Thomasetal.,
2002)
RETROICOR(Gloveretal.,
2000)
HeartRate
Image-basedPhysiologicalNoiseCorrection
Respiratory&CardiacPhase
Breathing&CardiacFrequency(~0.25Hz,~1Hz)
Model-basedUsingPeripheralData
CORSICA(Perlbarg etal.,2007)
TemporalPriorsonNoiseSpectrum
SpatialPriorsonNoiseLocation
FourierExpansion
Pre-MeasuredResponseFunctions
Cardiac(Chang&
Glover,2009)
Respiratory(Birnetal.,
2006)
RespiratoryVolume/Time
CSFPools(Flow)Vessels(Pulsation)
WhiteMatter(non-BOLD)
FIX(Salimi-Khorshidietal.,2014)
Multi-subjectdictionary(hierarchicalclassifier)
StochasticStateSpaceModel
DRIFTER(Särkkäetal.,
2012))
RespiratoryandCardiacTime
Course
aCompCor(Behzadi etal.,
2007)
Motion Models +
Censoring
2017-11-21 31
![Page 32: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/32.jpg)
Model-based Phys Noise Correction
Lars Kasper: fMRI Noise Models & Correction
Exploratory
SpatialICA(Thomasetal.,
2002)
RETROICOR(Gloveretal.,
2000)
HeartRate
Image-basedPhysiologicalNoiseCorrection
Respiratory&CardiacPhase
Breathing&CardiacFrequency(~0.25Hz,~1Hz)
Model-basedUsingPeripheralData
CORSICA(Perlbarg etal.,2007)
TemporalPriorsonNoiseSpectrum
SpatialPriorsonNoiseLocation
FourierExpansion
Pre-MeasuredResponseFunctions
Cardiac(Chang&
Glover,2009)
Respiratory(Birnetal.,
2006)
RespiratoryVolume/Time
CSFPools(Flow)Vessels(Pulsation)
WhiteMatter(non-BOLD)
FIX(Salimi-Khorshidietal.,2014)
Multi-subjectdictionary(hierarchicalclassifier)
StochasticStateSpaceModel
DRIFTER(Särkkäetal.,
2012))
RespiratoryandCardiacTime
Course
aCompCor(Behzadi etal.,
2007)
2017-11-21 32
![Page 33: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/33.jpg)
Noise Modeling
Cardiac/respiratory
phase
Lars Kasper: fMRI Noise Models & Correction
RespiratoryResponse Function
RETROspectiveImage CORrection
Cardiac Response Function
Heart Rate Resp. Volume
per Time
convolved with
CRF
convolved with
RRF
Fourier expansion
(cosine/sine)
evaluated at 1 time point (slice) per volume =
regressor
2017-11-21 33
![Page 34: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/34.jpg)
Noise Modeling
Lars Kasper: fMRI Noise Models & Correction
RespiratoryResponse Function
RETROspectiveImage CORrection
Cardiac Response Function
Cardiac/respiratory phase
2017-11-21 34
![Page 35: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/35.jpg)
Model: Fourier Phase Expansion
Cosine and sine to allow for constant phase shifts per voxel
Higher model orders to account for under-sampling of
physiological frequencies with typical TR in fMRI
Lars Kasper: fMRI Noise Models & Correction
physiological regressors matrix for GLM
- specified regressors orthogonalized -
regressor
scan volu
me
5 10 15 20
50
100
150
200
250
300
350
400
450
cos φ sin φ cos 2φ sin 2φ cos 3φ sin 3φ
scans
2017-11-21 35
![Page 36: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/36.jpg)
Aliasing of Physiology
Lars Kasper: fMRI Noise Models & Correction
Courtesy: R. Birn, HBM 2015
2017-11-21 36
![Page 37: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/37.jpg)
Noise Modeling
Lars Kasper: fMRI Noise Models & Correction
RespiratoryResponse Function
RETROspectiveImage CORrection
Cardiac Response Function
Heart Rate Heart Rate Variability
Response Regressor convolved with
CRF
2017-11-21 37
![Page 38: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/38.jpg)
Noise Modeling
Lars Kasper: fMRI Noise Models & Correction
RespiratoryResponse Function
RETROspectiveImage CORrection
Cardiac Response Function
Respiratory
Volume per Time convolved with
RRF
Respiratory Volume
per Time Regressor
2017-11-21 38
![Page 39: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/39.jpg)
Exploratory Phys Noise Correction
Lars Kasper: fMRI Noise Models & Correction
Exploratory
SpatialICA(Thomasetal.,
2002)
RETROICOR(Gloveretal.,
2000)
HeartRate
Image-basedPhysiologicalNoiseCorrection
Respiratory&CardiacPhase
Breathing&CardiacFrequency(~0.25Hz,~1Hz)
Model-basedUsingPeripheralData
CORSICA(Perlbarg etal.,2007)
TemporalPriorsonNoiseSpectrum
SpatialPriorsonNoiseLocation
FourierExpansion
Pre-MeasuredResponseFunctions
Cardiac(Chang&
Glover,2009)
Respiratory(Birnetal.,
2006)
RespiratoryVolume/Time
CSFPools(Flow)Vessels(Pulsation)
WhiteMatter(non-BOLD)
FIX(Salimi-Khorshidietal.,2014)
Multi-subjectdictionary(hierarchicalclassifier)
StochasticStateSpaceModel
DRIFTER(Särkkäetal.,
2012))
RespiratoryandCardiacTime
Course
aCompCor(Behzadi etal.,
2007)
2017-11-21 39
![Page 40: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/40.jpg)
Noise Component Modeling
Use priors about physiological noise to identify noise
components (time series)
Spatial Priors: Mechanisms of physiological noise implicate
physiological noise in CSF, blood vessels
Temporal Priors: Knowledge about typical physiological
frequency contents (heart ~ 1Hz, breathing 0.2-0.4 Hz)
Note that simple filtering is impossible (cf. aliasing)
Population Priors: Use dictionary learning from manually
labellled training set of subjects (FIX)
Lars Kasper: fMRI Noise Models & Correction2017-11-21 40
Exploratory
SpatialICA(Thomasetal.,
2002)
RETROICOR(Gloveretal.,
2000)
HeartRate
Image-basedPhysiologicalNoiseCorrection
Respiratory&CardiacPhase
Breathing&CardiacFrequency(~0.25Hz,~1Hz)
Model-basedUsingPeripheralData
CORSICA(Perlbarg etal.,2007)
TemporalPriorsonNoiseSpectrum
SpatialPriorsonNoiseLocation
FourierExpansion
Pre-MeasuredResponseFunctions
Cardiac(Chang&
Glover,2009)
Respiratory(Birnetal.,
2006)
RespiratoryVolume/Time
CSFPools(Flow)Vessels(Pulsation)
WhiteMatter(non-BOLD)
FIX(Salimi-Khorshidietal.,2014)
Multi-subjectdictionary(hierarchicalclassifier)
StochasticStateSpaceModel
DRIFTER(Särkkäetal.,
2012))
RespiratoryandCardiacTime
Course
aCompCor(Behzadi etal.,
2007)
![Page 41: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/41.jpg)
PCA VS ICA
Methods to extract components (i.e. summarize
ROIs/spectra) differ:
Maximum variance time series: Principal Component Analysis
(PCA) from region of interest (aCompCor, Behzadi 2007)
Maximally independent time courses/sites: spatial/temporal ICA,
FSL MELODIC, FIX
aCompCor is basically identical to a seed-based
correlation analysis in resting-state fMRI
Here: seed is in region-of-no-interest and correlated time series
regressed out
See previous talk (resting state analysis) for more details
Lars Kasper: fMRI Noise Models & Correction2017-11-21 41
![Page 42: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/42.jpg)
Preprocessing Techniques
FSL MELODIC, FIX
Lars Kasper: fMRI Noise Models & Correction
Cardiac
2017-11-21 42
![Page 43: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/43.jpg)
Other Physiological Corrections
Non-linear models
DRIFTER: Kalman Filter, Bayesian, Joint Stochastic State-space
model of peripheral physiology and BOLD
Identify noise via task test-retest reproducibility
PHYCAA: e.g. via high-freq. autocorrelation, anatomy
GLMDenoise: PCA of noise regressors
MEICA: Multi-Echo ICA
Use diff. TE-images to decompose
proton density from T2* changes
Lars Kasper: fMRI Noise Models & Correction
Särkkä, NeuroImage, 2012
Churchill, NeuroImage, 2012/13
Kay, Front. Neurosc., 2013
Olafsson, NeuroImage, 2015
2017-11-21 43
![Page 44: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/44.jpg)
Outline – Noise Correction
MRI Time Series Recap and Noise Sources
Why de-noising? Structured Noise; Noise Pathways
Noise Correction Approaches
Target: Scanner Drift, Motion, Cardiac/Breathing Cycle
Method: Modeling VS Preprocessing
Input: fMRI Data VS Peripheral Measures
Prospects for Improving Group Statistics
Limitations
Degrees of Freedom; Task-related “noise”; Interoception
Lars Kasper: fMRI Noise Models & Correction2017-11-21 44
![Page 45: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/45.jpg)
When? – Literature Evidence
Resting-state: Birn, R. M. “The Role of Physiological
Noise in Resting-state Functional
Connectivity.” NeuroImage 62, 2012
Birn, R. M., et al. “Separating
Respiratory-variation-related
Fluctuations from Neuronal-activity-
related Fluctuations in fMRI.”
NeuroImage 31, 2006
Task-based: Hutton, C., et al. “The Impact of
Physiological Noise Correction on
fMRI at 7 T.” NeuroImage 57, 2011:
Lars Kasper: fMRI Noise Models & Correction2017-11-21 45
![Page 46: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/46.jpg)
Lars Kasper: fMRI Noise Models & Correction
Physiological noise correction not a default pre-
processing step in task-based fMRI
Reasons
Impact on group level fMRI
no reports for non-trivial paradigms
Existing Toolboxes lack…
robust, automatic implementation
dealing with variable peripheral data quality
All these methods, but…
46
![Page 47: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/47.jpg)
Paradigm: Learning from Advice
Lars Kasper: fMRI Noise Models & Correction
Diaconescu et al, 2014, PLoS Comp. Biol.
Hierarchical learning of trustworthyness
of advisor over time
Contrasts: Prediction and Prediction Error about advice
2017-11-21 47
![Page 48: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/48.jpg)
Group Level Impact PhysIO
Andreea Diaconescu (TNU): Social Learning Experiment 2012-
2014, (N=35)
F-contrast: Where does physiological noise model explain
significant variance?
Lars Kasper: fMRI Noise Models & Correction2017-11-21 48
![Page 49: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/49.jpg)
Relevance for Neuromodulation
cardiac (red), respiratory (blue), cardXresp (green)
Lars Kasper: fMRI Noise Models & Correction2017-11-21 49
![Page 50: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/50.jpg)
Relevance for Neuromodulation
VTA (DA)
Lars Kasper: fMRI Noise Models & Correction
Locus coeruleus (NA)
Raphe Nuclei (5-HT)
2017-11-21 50
![Page 51: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/51.jpg)
Effects on Group Contrasts
Lars Kasper: fMRI Noise Models & Correction
Higher Sensitivity False Positives
2nd level t-contrast
Social Prediction Error2017-11-21 51
![Page 52: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/52.jpg)
Outline – Noise Correction
MRI Time Series Recap and Noise Sources
Why de-noising? Structured Noise; Noise Pathways
Noise Correction Approaches
Target: Scanner Drift, Motion, Cardiac/Breathing Cycle
Method: Modeling VS Preprocessing
Input: fMRI Data VS Peripheral Measures
Prospects for Improving Group Statistics
Limitations
Degrees of Freedom; Task-related “noise”; Interoception
Lars Kasper: fMRI Noise Models & Correction2017-11-21 56
![Page 53: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/53.jpg)
Limitations of Noise Modeling
Degrees of freedom, sensitivity reduced by too many
ineffective regressors
F-test informative
Intrinsic correlations of functional areas of interoception
and peripheral physiology
E.g. Amygdala, Insula, ACC
Controversial reading:
fMRI of the Amygdala: All In Vein? – Neuroskeptic
Alternative: Masking, Pure anatomical priors removing CSF,
angiography (vessels)
Lars Kasper: fMRI Noise Models & Correction2017-11-21 57
![Page 54: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/54.jpg)
Conclusion
MRI Time Series and
Physiological Noise
Image-Based Correction in
the GLM
Noise Modeling Prospects:
Group FX
The PhysIO Toolbox
Structured noise through
cardiac/resp cycle (70%)
Nuisance regressors from
Fourier expansion, response
functions
Increase group sensitivity (low
inter-subject variability), fewer
false positives
Correction in SPM/Matlab in
practice => NOW!
Lars Kasper: fMRI Noise Models & Correction2017-11-21 58
![Page 55: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/55.jpg)
Practical Session
Demo: The PhysIO Toolbox for Physiological Noise
Correction in fMRI
Features and Workflow
Image-based physiological noise correction in the GLM
RETROICOR, HRV, RVT
Noise-ROIs
Practical Demo (SPM Batch)
Estimating different Models
Understanding the Preprocessing Plots
Automatic Model Assessment, Diagnostics on Contrast
2017-11-21 59Lars Kasper: fMRI Noise Models & Correction
![Page 56: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/56.jpg)
Image-based Noise Correction
Lars Kasper: fMRI Noise Models & Correction
PhysIO Toolbox
Exploratory
SpatialICA(Thomasetal.,
2002)
RETROICOR(Gloveretal.,
2000)
HeartRate
Image-basedPhysiologicalNoiseCorrection
Respiratory&CardiacPhase
Breathing&CardiacFrequency(~0.25Hz,~1Hz)
Model-basedUsingPeripheralData
CORSICA(Perlbarg etal.,2007)
TemporalPriorsonNoiseSpectrum
SpatialPriorsonNoiseLocation
FourierExpansion
Pre-MeasuredResponseFunctions
Cardiac(Chang&
Glover,2009)
Respiratory(Birnetal.,
2006)
RespiratoryVolume/Time
CSFPools(Flow)Vessels(Pulsation)
WhiteMatter(non-BOLD)
FIX(Salimi-Khorshidietal.,2014)
Multi-subjectdictionary(hierarchicalclassifier)
StochasticStateSpaceModel
DRIFTER(Särkkäetal.,
2012))
RespiratoryandCardiacTime
Course
aCompCor(Behzadi etal.,
2007)
Motion Models +
Censoring
2017-11-21 60
![Page 57: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/57.jpg)
The PhysIO Toolbox
Developed at the Translational Neuromodeling Unit (TNU)
since 2008
Lead programmer: Lars Kasper (TNU)
Contributors: Jakob Heinzle (TNU), Steffen Bollmann (KiSpi Zurich)
Part of the TNU «TAPAS» software suite
Used at the TNU, in Zurich and beyond by ~50 researchers
Iglesias 2013, Neuron; Kasper 2014, NeuroImage; Bollmann 2014, PhDThesis;
Sulzer 2013, NeuroImage; Hauser 2014, NeuroImage; Grueschow 2015, Neuron
Download & Example Data:
https://www.tnu.ethz.ch/en/software/tapas.html
https://www.tnu.ethz.ch/en/software/tapas/data.html
61Lars Kasper: fMRI Noise Models & Correction2017-11-21
![Page 58: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/58.jpg)
Workflow of the PhysIO Toolbox
2017-11-21 62Lars Kasper: fMRI Noise Models & Correction
![Page 59: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/59.jpg)
Flowchart of Noise Correction
2017-11-21 63Lars Kasper: fMRI Noise Models & Correction
![Page 60: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/60.jpg)
Scan Sync with Philips Gradients
2017-11-21 64Lars Kasper: fMRI Noise Models & Correction
![Page 61: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/61.jpg)
Data Preprocessing Overview
2017-11-21 65Lars Kasper: fMRI Noise Models & Correction
![Page 62: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/62.jpg)
Preprocessing: Peak Detection
2017-11-21 66Lars Kasper: fMRI Noise Models & Correction
![Page 63: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/63.jpg)
Peak Detection: Robustness
2017-11-21 67Lars Kasper: fMRI Noise Models & Correction
![Page 64: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/64.jpg)
Noise Modeling
2017-11-21 68Lars Kasper: fMRI Noise Models & Correction
![Page 65: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/65.jpg)
Diagnostics: Model Assessment
2017-11-21 69Lars Kasper: fMRI Noise Models & Correction
![Page 66: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/66.jpg)
Model Check: SPM F-contrasts
Lars Kasper: fMRI Noise Models & Correction 70
Check Influence of Physiological Noise (Correction) on Data
• SPM
• F-contrast on 1st and second level
Finally:
![Page 67: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/67.jpg)
Flexibility: Scanner vendors
2017-11-21 71Lars Kasper: fMRI Noise Models & Correction
![Page 68: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/68.jpg)
References
Birn, Rasmus M., Jason B. Diamond, Monica A. Smith, and Peter A. Bandettini. 2006. “Separating Respiratory-
variation-related Fluctuations from Neuronal-activity-related Fluctuations in fMRI.” NeuroImage 31 (4) (July 15):
1536–1548. doi:10.1016/j.neuroimage.2006.02.048.
Glover, G H, T Q Li, and D Ress. 2000. “Image-based Method for Retrospective Correction of Physiological Motion
Effects in fMRI: RETROICOR.” Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic
Resonance in Medicine / Society of Magnetic Resonance in Medicine 44 (1) (July): 162–7.
Harvey, Ann K., Kyle T.S. Pattinson, Jonathan C.W. Brooks, Stephen D. Mayhew, Mark Jenkinson, and Richard G.
Wise. 2008. “Brainstem Functional Magnetic Resonance Imaging: Disentangling Signal from Physiological Noise.”
Journal of Magnetic Resonance Imaging 28 (6): 1337–1344. doi:10.1002/jmri.21623.
Hutton, C., O. Josephs, J. Stadler, E. Featherstone, A. Reid, O. Speck, J. Bernarding, and N. Weiskopf. 2011. “The
Impact of Physiological Noise Correction on fMRI at 7 T.” NeuroImage 57 (1) (July 1): 101–112.
doi:10.1016/j.neuroimage.2011.04.018.
Josephs, O., Howseman, A.M., Friston, K., Turner, R., 1997. “Physiological noise modelling for multi-slice EPI fMRI
using SPM.” Proceedings of the 5th Annual Meeting of ISMRM, Vancouver, Canada, p. 1682
Kasper, L., Bollmann, S., Diaconescu, A.O., Hutton, C., Heinzle, J., Iglesias, S., Hauser, T.U., Sebold, M., Manjaly, Z.-
M., Pruessmann, K.P., Stephan, K.E., 2016. The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data.
Journal of Neuroscience Methods accepted. doi:10.1016/j.jneumeth.2016.10.019
Lars Kasper: fMRI Noise Models & Correction2017-11-21 72
![Page 69: Noise Models and Correction for fMRI - TNU · Lars Kasper: fMRI Noise Models & Correction Magnetization Cardiac Cycle Breathing Cycle Noise Generator Entry Points of Noise Mediating](https://reader036.vdocuments.us/reader036/viewer/2022070802/5f02c3197e708231d405e289/html5/thumbnails/69.jpg)
fMRI = Acquiring Movies
…of three-
dimensional Blood
Oxygen-Level
Dependent (BOLD)
contrast images
Lars Kasper: fMRI Noise Models & Correction
Run/Session:
Time Series of
Images
y
x
z
…
scan 1 time scan N
Task TaskNo Task
2017-11-21 73