PhD defence, November 2, 2021
Stefano Moia
Supervisors:
Dr. César Caballero-Gaudes
Dr. Maite Termenón
Cerebrovascular Reactivity (CVR) is the response of cerebral vessels to a vasoactive stimulus (e.g. CO2) to provide sufficient O2 to cerebral tissues¹
1. Liu et al. 2018 (Neuroimage); 2. Pinto et al. 2021 (Front. Physiol.)
CVR can be measured during BOLD fMRI experiments with Breath-holds (BH), that induce the subject into a state of hypercapnia²
The vessels dilate → Increase of blood flow → Increase of %BOLD signal
CVR mapping [%BOLD/mmHg] can be obtained through a linear regression analysis using the recordings of exhaled CO2 (reliable proxy of CO2 partial pressure in arterial blood)
Two problems:
Motion
CO2
BOLD
Two problems:
Motion
CO2
BOLD
Different methods have been proposed to take into account the lag of CVR:
cross-correlation (RIPTiDe)¹,
Lagged GLM (L-GLM)²,
bayesian estimation³, ...
1. Frederick et al. 2012 (NeuroImage); 2. Sousa et al. 2014 (NeuroImage)
3. https://github.com/physimals/quantiphyse-cvr; 4. Moia, Stickland, et al. 2020 (EMBC)
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An important factor to take into account is to set up denoising and CVR estimation simultaneously⁴
[Moia, Stickland, et al. 2020 (EMBC)]
1. Frederick et al. 2012 (NeuroImage); 2. Sousa et al. 2014 (Neuroimage)
Different methods have been proposed to take into account the lagged CVR:
Performing denoising in sequential steps, rather than in parallel, might reintroduce removed artefacts
Lindquist et al. 2019 (Hum. Brain Mapp.)
CVR and lag maps: L-GLM with each lagged regressor and nuisance regressors (12 motion parameters and low frequency trends), voxelwise selection of the lagged model with highest explained variance (R²), normalisation to MNI152 template (2.5 mm isotropic)
We compared four pipelines:
We compared four pipelines:
CNR of lag maps | SimMot | SeqMot | NoMot |
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GM-WM | 0.52 ±0.21 | 0.46 ±0.26 | 0.49 ±0.25 |
GM-Putamen | 0.47 ±0.22 | 0.44 ±0.21 | 0.44 ±0.21 |
GM-Cerebellum | 0.82 ±0.15 | 0.69 ±0.17* | 0.69 ±0.16* |
Non optimising leads to underestimate the CVR, especially in subcortical areas.
Lag maps show anatomical consistency
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Different lag responses, coherent with previous evidence (e.g. Putamen has earlier response than GM)
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Area mostly affected by motion! →
Moia, Stickland, et al. 2020 (EMBC)
For comparison:
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optimised CVR map and lag map
Independent Component Analysis (ICA) is commonly used to remove motion effects and other sources of noise from fMRI data
Motion
Motion + MB artefact
CSF pulsations
Griffanti et al. 2014 (NeuroImage), 2017 (NeuroImage), The tedana Community et al. 2021 (Zenodo)
Multi Echo (ME): we collect the signal multiple times at different TEs to obtain n timeseries per voxel
TR
BOLD [a.u.]
Multi Echo (ME): we collect the signal multiple times at different TEs to obtain n timeseries per voxel
TR
BOLD [a.u.]
For each voxel and TR, we can Optimally Combine the echo volumes with a weighted sum based on their contribution to \( T_2^{\star} \)
In this way, spatial CNR and tSNR are maximised and the signal can be recovered in areas of drop-out
Posse et al. 1999 (Magn Reson Med)
Assuming monoexponential decay, we can express the
signal percentage change as:
\[ S_{SPC} \approx \Delta\rho - TE \cdot \Delta R_2^{\star} + n \quad where \enspace R_2^{\star} = \frac{1}{T_2^{\star}} \]
This let us differentiate BOLD-related (\(\Delta R_2^{\star}\)) from non-BOLD related (\(\Delta\rho\)) changes
Kundu et al. 2012 (NeuroImage)
If we apply ICA, we can fit the timeseries of the components to either sub-models and automatically classify them
What is the best way to denoise BH data after ICA?
being too aggressive might remove the signal of interest,
but being too conservative might keep too much noise in the model.
* TR = 1.5 s, TEs = 10.6/28.69/46.78/64.87/82.96 ms, MB acceleration factor = 4, GRAPPA = 2, voxel size = 2.4x2.4x3 mm³
10 neurotypical subjects
(5F, age 25-40y)
10 sessions, one week apart, same time of the day
BH paradigm: ME-fMRI (Gradient Echo EPI)
+ SBREF image
T2w, MP2RAGE (T1w), 4 RS,
3 tasks, and BH paradigm
CO2 and O2
sampling
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Functional:
CO2 traces:
What is the best way to denoise BH data after ICA?
being too aggressive might remove the signal of interest,
but being too conservative might keep too much noise in the model.
We set up a simultaneous estimation and denoise step, considering motion parameters,
their derivative, Legendre polynomials to the fourth order, and:
We compared:
What is the best way to denoise the data after ICA?
Regression based:
Aggressive approach: nuisance regression using only the rejected components.
Non aggressive (partial regression) approach: all the components are considered, but only the rejected components are regressed out of the data.
Orthogonalised approach: the rejected components are orthogonalised with respect to the other components.
4D-based approach (similar to M/EEG): reconstruct volumes on noise, then subtract it from the original data.
\( Y = \) \(A\) \(+\) \(R\) \(+ n \)
Multivariate:
Effect of denoising approach is significant for slope (F(5,354)=177.6, p<0.001) and intercept (F(5,354)=225.7, p<0.001) of the linear regression model
DVARS vs FD
Group level, DVARS vs FD
Slope
Intercept
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Average % BOLD and DVARS across all trials
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Aggressive denoise removes signal of interest
OC and E-02 denoise affects the signal of interest more than ICA denoise
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Lag reliability
CVR reliability
Moia et al. 2021 (NeuroImage)
\( \cdot \) timepoint \( - \) session
Moia et al. 2021 (NeuroImage)
Moia et al. 2021 (NeuroImage)
Moia et al. 2021 (NeuroImage)
Moia et al. 2021 (NeuroImage)
CVR amplitude
CVR lag
CVR amplitude
CVR lag
Moia et al. 2021 (NeuroImage)
CVR amplitude
CVR lag
CVR amplitude
CVR lag
Moia et al. 2021 (NeuroImage)
CVR amplitude
CVR lag
CVR amplitude
CVR lag
Moia et al. 2021 (NeuroImage)
ME-CON should be better than OC-MPR in temporal-dependent application
Example of application: timeseries clustering (Self-Organising Maps, 20 clusters)
Submitted to ISMRM 2022
In data characterised by global responses and high motion collinearity, such as CVR, a conservative ICA-based approach best removes motion-related effects, while obtaining reliable responses, but a simple optimal combination of ME data provides similar estimations
However, further examinations are required to translate these observations to paradigms with lower collinear motion and more focal responses (e.g. functional task), or in which there is no task information available (e.g. rest)
We plan to repeat the same experiment with the other acquisitions in EuskalIBUR, considering both statistical maps and temporal properties (e.g. connectome)
Due to its nature as homeostatic and cerebrovascular process, CVR is modulated by systemic changes in blood pressure¹
1. Fierstra et al. 2013 (J. Physiol.); 2. e.g. Hetzel et al. 1999 (Stroke)
Previous studies with Transcranial Doppler Ultrasound suggest to take into account blood pressure when measuring CVR²
To our knowledge, the impact of blood pressure on BOLD-fMRI based CVR estimation has not been assessed yet
10 neurotypical subjects
(5F, age 25-40y) (3 discarded)
10 sessions, one week apart, same time of the day
Vital signs (VS), measured before the MRI session, while the subject was lying supine on a bed, once on the left arm and once on the right arm:
We averaged the two measurements and computed the Mean Arterial Pressure (MAP) and the Pulse Pressure (PP):
We used 3dLMEr¹ to set up the following LME models:
Results were thresholded at \(p<0.05\) after controlling for false discovery rate²
1. Chen et al. 2013 (Neuroimage); 2. Benjamini et al. 2006 (Biometrika)
*maps were smoothed 5mm FWHM
We smooth CVR and lag maps using a dilated GM mask (white mask below) and a FWHM of 5mm (voxel size 2.5 isometric) before running 3dLMEr.
Both MAP and PP should be taken into account in CVR experiments, especially in comparisons between subjects or between regions!
1. Kastrup et al. 1997, 1998 (Stroke), Tallon et al. 2020 (Exp. Psychol.); 2. Kassner et al. 2010 (J. Magn. Reson. Imaging)
3. Chen et al. 2021 (Int. J. Imaging Syst. Technol.), Jiménez Caballero et al. 2006 (Rev Neurol)
2. Golestani et al. 2016 (NeuroImage)
Estimating CVR with a BH task requires compliant subjects and
dedicated equipment, making it harder to adopt in clinical practice
As a cheaper and feasible alternative, previous literature suggests to use
Resting State fluctuations measures (RSF), such as:
1. Kannurpatti et al. 2014 (PloS ONE)
Text
[Zou et al. 2013 (Hum. Brain Mapp.)]
[Kannurpatti et al. 2014 (PLoS ONE)]
[Mennes et al. 2011 (NeuroImage)]
We preprocessed RS, motor, and Simon data similarly to CVR
We computed:
We selected:
Results were thresholded at \(p<0.05\) after controlling for false discovery rate³
(then at \(p<0.001\) uncorrected)
1. Chen et al. 2013 (Neuroimage); 2. Golestani et al. 2016 (NeuroImage); 3. Benjamini et al. 2006 (Biometrika)
We used 3dLMEr¹ to set up the following LME models voxelwise (R syntax):
We used the first model considering the average GM value of RSF and CVR²
We used 3dLMEr¹ to set up the following LME models (R syntax):
Only sex had a significant effect on RSF
Golestani et al. 2016 (NeuroImage)
Motor task
Simon task, congruent responses
Simon task, incongruent responses
This observation does not translate automatically to paradigms with lower collinear motion and more focal responses (e.g. functional task), or in which there is no task information available (e.g. rest)
Further comparisons are also necessary to compare the performance of different lagged approaches in a multiverse environment
The failure of generalisation of previous observations might be related to different methods, but whether this is related to a better denoising and signal quality or to a possibly non optimal setting (e.g. compared to gas challenges) is uncertain
A different statistical perspective (i.e. Bayesian) is required to exclude any relationship between CVR and RS fluctuations, and further analyses are required to improve the agreement between CVR and RS fluctuations
It's a vascular response that maintains the adequate levels of oxygen (and pH)
By acquiring ME data and using a Lagged GLM to estimate it
Blood pressure seems to have localised effects, as well as sex
Although it cannot be excluded, the impact of CVR on RSF might be highly subject specific, while the impact of CVR on tIA requires further analysis to be ascertained
...the SPiN-lab group @ BCBL
... the Brightlab - ANVIL group @ Northwestern University
...my family and my friends
Research supported by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the National Institutes of Health under award number K12HD073945, the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant agreement No. 713673), a fellowship from La Caixa Foundation (ID 100010434, fellowship code LCF/BQ/IN17/11620063), the Spanish Ministry of Economy and Competitiveness (Ramon y Cajal Fellowship, RYC-2017- 21845), the Spanish State Research Agency (BCBL “Severo Ochoa” excellence accreditation, SEV- 2015-490), the Basque Government (BERC 2018-2021 and PIBA_2019_104), the Spanish Ministry of Science, Innovation and Universities (MICINN; FJCI-2017-31814)
... Dr. César Caballero-Gaudes, Dr. Maite Termenon, and Dr. Molly G. Bright
...you for the (sustained) attention!