Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes...
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Transcript of Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes...
![Page 1: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/1.jpg)
Cluster Analysis of fMRI Data Using Dendrogram
Sharpening
L. Stanberry, R. Nandy, and D. Cordes
Presenter: Abdullah-Al Mahmood
![Page 2: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/2.jpg)
Outline
Problem DefinitionThe Solution
Choice of methods, parameters etc.Algorithm – Dendrogram Sharpening
Experiments and ResultsDiscussion
![Page 3: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/3.jpg)
The Task
Identify areas of activation in the brain in response to certain stimuli
![Page 4: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/4.jpg)
The Task
Identify areas of activation in the brain in response to certain stimuli
Simple case: Single StimulusPaced motor paradigm (finger
tapping)Region of Interest: Motor cortex
(Motion controlling area)
![Page 5: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/5.jpg)
The Task
Identify areas of activation in the brain in response to certain stimuli
Simple case: Single StimulusPaced motor paradigm (finger
tapping)Region of Interest: Motor cortex
(Motion controlling area)Challenges: Noise & Data Volume
![Page 6: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/6.jpg)
Basic Algorithm
Hierarchical clustering
![Page 7: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/7.jpg)
Basic Algorithm
Hierarchical clusteringFactors to consider
The (dis)similarity measureThe linkage methodThreshold for cutting tree vs. number of nodes
![Page 8: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/8.jpg)
Distance Measure
Two voxels are similar if the activation patterns are similarCorrelation coefficient of the time courses measures similarityDistance between voxels i and j
d(i, j ) = 1 – corr. coeff.(T (i ), T ( j ))
Not a metric
![Page 9: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/9.jpg)
Linkage Methods
Single – distance between closest pair of points of two clustersAverage – average distance of all pairs of points, one from each clusterComplete – largest distance between two points in two clustersSingle linkage is used in this work
![Page 10: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/10.jpg)
Single Linkage Dendrogram (SLD)
ProsCorrectly identifies structure when clusters overlapInvariant under reordering of objectsComputationally simple
Cons“Chaining effect” – highly dissimilar size of children nodes
![Page 11: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/11.jpg)
Dendrogram Example - I
![Page 12: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/12.jpg)
Dendrogram Example - II
![Page 13: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/13.jpg)
Dendrogram Sharpening
Removes chaining effect and reveals “interesting” structureDiscards some points in the process that are attached to clusters laterTwo parameters
ncore for a node/cluster (large value)
nfluff for its children (small value)
![Page 14: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/14.jpg)
Dendrogram Sharpening
The Basic AlgorithmForm a queue of nodes (initially containing root cluster only)While not empty(queue) dequeue node
If size(node) < ncore discard all points under it.Else discard child(ren) with size < nfluff and queue the remaining child(ren).
![Page 15: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/15.jpg)
Sharpening Example - I
![Page 16: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/16.jpg)
Sharpening Example - II
![Page 17: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/17.jpg)
Cluster Identification
Method of inconsistent edgesMeasure of inconsistencyThreshold = Median + 2(Upper-hinge
value – Lower-hinge value)
Upper and lower values correspond to first and third quartile values (ascending order sort for distance)
![Page 18: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/18.jpg)
Experimental Parameters
Paradigm I4 slices, each of 6464 resolution, 750 time points
Paradigm 220 slices, each of 6464 resolution, 165 time points
Activity and rest period alternated
![Page 19: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/19.jpg)
Data reduction
Discard voxels with SNR value (= mean signal intensity standard deviation) in the first decileDiscard voxels with correlation value below 0.5 (normalized series with mean 0 and std. dev. = 1) or having less than 5 significant correlations
![Page 20: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/20.jpg)
Once Sharpened Data (P – I)
![Page 21: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/21.jpg)
Twice Sharpened Data (P – I)
![Page 22: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/22.jpg)
Final classification (P – I)
![Page 23: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/23.jpg)
Map from SPM analysis
![Page 24: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/24.jpg)
A cluster from Paradigm II
![Page 25: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/25.jpg)
Numerical Comparison
![Page 26: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/26.jpg)
Discussion
Dendrogram sharpening can help in identifying clusters quite wellCan be applied to raw data as well as preprocessed dataNot tested for weak/multiple stimuliNeeds parameter tuning for sharpening algorithm
![Page 27: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/27.jpg)
Reference
L. Stanberry, R. Nandy and D. Cordes Cluster Analysis of fMRI Data Using Dendrogram Sharpening. Human Brain Mapping, 20:201-219, 2003.
N.B. All figures and tables are taken from the original work
![Page 28: Cluster Analysis of fMRI Data Using Dendrogram Sharpening L. Stanberry, R. Nandy, and D. Cordes Presenter: Abdullah-Al Mahmood.](https://reader036.fdocuments.in/reader036/viewer/2022062223/551b3a5a550346ae7a8b46a6/html5/thumbnails/28.jpg)
Questions?