Date post: | 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?
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?
Following examples taken from:
Cortex reconstruction
• Plenty of available software packages– Brain Voyager– Free Surfer– …
Identification of gray matter
Reconstruction of cortical surface
Visualization on inflated and flattened brains
Bar et al PNAS 2006
Hasson et al Science 2004
Translating data & ROIs: misalignment = missed data
Successful selection of gray matter ROI
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
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
Dealing with EPI distortion in defining ROIs
EPI aligned to reference anatomy
EPI aligned to distorted reference anatomy
Cortex reconstruction on distorted anatomy(the hard way to solve the problem)