Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree...
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Transcript of Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree...
![Page 1: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/1.jpg)
Joint Detection-Estimation of Brain Activity in fMRI using
Graph Cuts
Thesis for the Master degree in Biomedical EngineeringLisbon, 30th October 2008
Joana Maria Rosado da Silva Coelho
![Page 2: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/2.jpg)
Contents:
1 Introduction
2 Objectives
3 Proposed Model
4 Results
5 Conclusions
![Page 3: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/3.jpg)
• fMRI technique aims at identifying cerebral areas (Brain Mapping) that were activated by an external stimulus – paradigm.
• Classical tasks to induce neuronal responses:• visual activation (looking at changing patterns);• sensorimotor activation (sequence of defined finger movements).
• This modality is based on the assumption that activated regions present increased metabolic activity.
functional MRI:
![Page 4: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/4.jpg)
• The higher proportion of hemoglobin molecules bound with oxygen (oxyhemoglobin) is observed as a signal increase on T2*- weighted images (increase in the BOLD signal).
• BOLD signal does not measure brain function directly.
fMRI-BOLD
Baseline Activation
![Page 5: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/5.jpg)
• After a stimulus application there is a local hemodynamic change in capillaries and draining veins.
• This vascular response can be modeled by an hemodynamic response function.
Hemodynamic Response Function
![Page 6: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/6.jpg)
Diagram of a typical fMRI data set.
Type of Data:
![Page 7: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/7.jpg)
Example of a time course from a visual stimulation experiment.
Type of Data:
![Page 8: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/8.jpg)
• Classical method: - Statistical parametric mapping (SPM) commonly based on GLM - 2 steps algorithm: Estimation and Inference - Inference step needs the tuning of the p-value
SPM-GLM
2211 xxy
![Page 9: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/9.jpg)
Contents:
1 Introduction
2 Objectives
3 Proposed Model
4 Results
5 Conclusions
![Page 10: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/10.jpg)
Objectives:
Estimate the hemodynamic response function (HRF)
Incorporate the drift removal
Statistical Model:
SPM-Drift-GC
Model spatial correlation
Detect activated regions
![Page 11: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/11.jpg)
Contents:
1 Introduction
2 Objectives
3 Proposed Model
4 Results
5 Conclusions
![Page 12: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/12.jpg)
Proposed Model:
Neuro-Hemodynamic
System
Stimuli BOLD Signal?
![Page 13: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/13.jpg)
Bayesian Approach – MAP criterion
The Maximum a Posteriori (MAP) estimation is obtained by computing
where
)()(),,,(),,,( idihiiiiyiiii dEhEdhbyEdhbyE
Data Fidelity Term Prior Term
),,,(minarg)ˆ,ˆ,ˆ(,,
iiiidhb
iii dhbyEdhbiii
![Page 14: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/14.jpg)
Algorithm
•For each voxel, the estimation of bi, hi
and di is performed iteratively.
•h0 is a gamma function as proposed by Friston et al in 1998 which provides a physiological reasonable waveform to the HRF.
![Page 15: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/15.jpg)
• The final step models spatial correlation.• Since different tasks activate different brain regions, it is less probable that non-activated voxels appear inside of an activated region and the converse is also true.• Avoids misclassification inside activated regions. • Energy function:
• Dp – cost of attributing the label to the pixel p
• Vh,v – cost of attributing the labels , to the N neighbour pixels
Nvh
SCv
SChvh
Pp
SCppp
SCpp VDE
,, ),(),(),(
Spatial correlation step
SCp
SCh SC
v
![Page 16: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/16.jpg)
Contents:
1 Introduction
2 Objectives
3 Proposed Model
4 Results
5 Conclusions
![Page 17: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/17.jpg)
Results – Synthetic dataSPM-Drift SPM-Drift-GC
![Page 18: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/18.jpg)
Results – Synthetic data
Example of an SNR=2 dB time course with the real and estimated drift.
![Page 19: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/19.jpg)
Motor task – Right foot
SPM-GC-Drift
Loose result SPM-GLM
Reference result SPM-GLM
Restrict result SPM-GLM
Results – Real data
![Page 20: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/20.jpg)
Verb generation task
Loose result SPM-GLM
Reference result SPM-GLM
Restrict result SPM-GLM
Results – Real data
SPM-GC-Drift
![Page 21: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/21.jpg)
Motor task – Tongue
Loose result SPM-GLM
Reference result SPM-GLM
Restrict result SPM-GLM
Results – Real data
SPM-GC-Drift
![Page 22: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/22.jpg)
Verb generation task
Loose result SPM-GLM
Reference result SPM-GLM
Restrict result SPM-GLM
Results – Real data
SPM-GC-Drift
![Page 23: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/23.jpg)
Results – Real data
![Page 24: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/24.jpg)
Contents:
1 Introduction
2 Objectives
3 Proposed Model
4 Results
5 Conclusions
![Page 25: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/25.jpg)
• The Bayesian framework combined with Graph Cuts algorithm improves the sensitivity in the detection of activated areas.
• The proposed algorithm does not require the tuning of any parameter by the clinician.
• The beta coefficients are considered to be binary.
• SPM-GC-Drift leads to similar results as the ones obtained by SPM-GLM. However, other brain activated regions were also detected which requires future analysis.
Conclusions
![Page 26: Joint Detection-Estimation of Brain Activity in fMRI using Graph Cuts Thesis for the Master degree in Biomedical Engineering Lisbon, 30 th October 2008.](https://reader037.fdocuments.in/reader037/viewer/2022103111/5518a4b7550346b31f8b49e9/html5/thumbnails/26.jpg)
• The present work has been published• 30th Annual International IEEE EMBS Conference in Vancouver, British Columbia, Canada• RecPad2008 – 14ª Conferência Portuguesa de Reconhecimento de Padrões
•… and submitted• Human Brain Mapping international journal
Thank you for your attention!!!
Conclusions