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)