fmri group natasha matthews, ashley parks, destiny miller, ziad safadi, dana tudorascu, julia...
TRANSCRIPT
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fMRI Group
Natasha Matthews, Ashley Parks, Destiny Miller, Ziad Safadi, Dana Tudorascu, Julia Sacher. Adviser: Mark Wheeler
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Aims
Learn to implement block and event-related fMRI experimental designs
Develop a thorough understanding of the major choice points in the analysis stream for fMRI data
Learn fMRI data post-processing: GLM and group analysis
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Block ER
Design
Pros:
High detection power due to response summation
Simple analysis
Con:
Can’t look at effects of single events (e.g., correct vs. incorrect trials; target present vs. absent)
Pros:
Good estimation of time courses and reasonable detection
Enables post hoc sorting (e.g., correct vs. incorrect; target present vs. absent)
Con:
Some loss of power for the contrast between trial types.
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Task: Median Nerve Stimulation
A nerve stimulation device is place on the subjects wrist above their median nerve
An electrical pulse is applied, resulting in activation of the nerve
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Data AcquisitionScanner : Siemens 3T Trio
Number of subjects: 3
Anatomical Scan
T1 (MPRAGE)Slices : 38Functional Scan (Block design)
Whole Brain ScanSlices : 38Volumes:144
Voxel Size : 4 mm x 4 mm x 3.2mmInterleaved AcquisitionTR : 2sT2* Contrast
Scanner : Siemens 3T Trio
Number of subjects: 3
Anatomical Scan
T1 (MPRAGE)Functional Scan (Event-related design)
Whole Brain ScanSlices : 38Volumes run 1: 256Volumes run 2: 256Voxel Size : 4 mm x 4 mm x 3.2mmInterleaved AcquisitionTR : 2sT2* Contrast
Scanner : Siemens 3T TrioNumber of subjects: 3
Anatomical Scan
T1 (MPRAGE)Slices : 38Voxel Size: 0.5mm x 0.5mm x 1.0mm
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Blocked Design
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…
Time 0 s……....……….22s…….32s…………54s……64s…………86s……..96s……………. …278s Task
Volumes……………….11.…….16..…….……27.……32..…………43.……...48.……………. …139 (+5 extra)
Rest Rest Rest Rest
ZAP ZAP ZAP
Median Nerve Stimulation Localizer Task DesignGoal: Determine Motor Cortex Activation Region for Event
Related Task
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Nerve Stimulation Localizer Task
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Data Preprocessing for individual subjectsData Format: convert scanner images to format readable by AFNI
Dicom data, reformat to BRICK & .HEAD
Time Shift (slice timing correction): interpolation of time series to a specific point in TR (Fourier transformation: most accurate).
Spatial Registration (motion correction): of all images in the time series to a base image: we chose 6th image of run (close to structural image).
Smoothing: We investigated 4mm, 8mm, 12mm.
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Spatial Smoothing
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Box-car Model
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Model Fit: No smoothing
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Model Fit: 4mm smooth
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Model Fit: 8mm smooth
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Model Fit: 12 mm smooth
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t-statistics in individual voxels in ROI
0
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4
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Nopreprocessing
0 4 8 12
41.36.27
44.37.29
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Beta coefficients in individual voxels in ROI
0
5
10
15
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25
Nopreprocessing
0 4 8 12
44.37.29
44.37.29
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Data Preprocessing: Preparing for group analysis
Normalize time series: Regression coefficients now expressed as % signal change. For each run divide each time point by the mean and multiply by 100.
Original data Normalized data
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Preparing data for group analysis
Registration to standard space: Can be done manually or automatically
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Atlas TemplatesTT_N27+tlrc: AKA “Colin brain”. One subject (Colin) scanned 27 times and averaged.
TT_avg152T1+tlrc: Montreal Neurological Institute template, average volume of 152 normal brains.
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Group t-test (zap > baseline)
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Event-related Design
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Event Related Design: Stimulation with 3 different frequencies
2 Hz
3.85 Hz
9 Hz
Zap ON 9.09 3.85 2.00
Inter-stimulus jitter - 2, 4, 6 seconds
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Data from a representative subject2 Hz 3.8 Hz 9 Hz
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Comparison of 9 Hz Event Related Design and Block Design
Bloc
k de
sign
Even
t rel
ated
des
ign
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Creation of ROI masks to explore event-related data
ROI from functional results (localizer task)
ROI based on atlas coordinates
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Time courses extracted from functionally defined ROI
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1 2 3 4 5 6 7 8 9 10
Time
Beta values
average_9Hz
average_4Hz
average_2Hz
Peak of the activation
Area under the curve
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Results of ANOVA on event related datausing the PEAK of the time course
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Results of ANOVA on event related datausing the AREA UNDER THE CURVE
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Thank you
Mark Wheeler
Seong-Gi Kim
Tomika Cohen
Rebecca Clark
Fellow MNTPers!