fmri: biological basis and experiment design lecture 21: anatomical rois cortex-based analysis...
Post on 21-Dec-2015
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fMRI: Biological Basis and Experiment DesignLecture 21: Anatomical ROIs
• Cortex-based analysis• Cortex reconstruction• Registration• Distortion
1 light year = 5,913,000,000,000 miles?
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Cortex-based analysis
• Theory: signal changes we care about are in gray matter– White matter dilutes responses– CSF and vessels add noise
• Method: define gray matter and restrict analysis
• Problem: how do we define gray matter?
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Following examples taken from:
Cortex reconstruction
• Plenty of available software packages– Brain Voyager– Free Surfer– …
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Identification of gray matter
Reconstruction of cortical surface
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Visualization on inflated and flattened brains
Bar et al PNAS 2006
Hasson et al Science 2004
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Translating data & ROIs: misalignment = missed data
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Successful selection of gray matter ROI
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Functional - anatomical alignment
• Standard procedure– Acquire 3 data sets
• reference anatomy (not necessarily same scan)
• EPI
• “inplane anatomy” (T1-weighted FLASH or T2-weighted TurboSE, with same slice prescription as EPI)
– Align “inplane anatomy” with reference anatomy
– Use this alignment information to
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Functional - anatomical alignment
• Better procedure– Acquire 2 or 3 data sets
• reference anatomy (not necessarily same scan)
• EPI
• Optional: “inplane anatomy” (T1-weighted FLASH or T2-weighted TurboSE, with same slice prescription as EPI)
– Either• Align EPI to reference anatomy
• Align EPI to inplane anatomy and then inplane to reference
– Use this alignment information to
![Page 11: FMRI: Biological Basis and Experiment Design Lecture 21: Anatomical ROIs Cortex-based analysis Cortex reconstruction Registration Distortion 1 light year](https://reader030.vdocuments.site/reader030/viewer/2022032521/56649d5f5503460f94a4038b/html5/thumbnails/11.jpg)
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Dealing with EPI distortion in defining ROIs
EPI aligned to reference anatomy
EPI aligned to distorted reference anatomy
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Cortex reconstruction on distorted anatomy(the hard way to solve the problem)