fMRI-Standard Preprocessing

1 Slice timing problem correction

2 Head motion correction

3 Skull stripping

4 Coregistration

 

5 Spatial Normalization


fMRI-Evoked

Overview of Pipeline

1

Estimate the task-driven BOLD response model

2

Create subject evoked response map using General Linear Model (GLM) analysis

3

Group-level statistics

Sample Figures

Group evoked response map of optogenetic stimulation on Striatum


fMRI-Resting State

1

Nuisance signal regression (6 degrees of motion parameter)

2

Frequency filtering (Typical range of band-pass filter: 0.01 ~ 0.1Hz)

3

Calculate resting state parameters: ALFF, ReHo, Seed-based connectivity, etc.

4

Group-level statistics

Sample Figures

Seed-based voxel-wise connectivity map from single subject (Wistar rat P80)

Default mode network

Seed location: CG

Primary Somatosensory

Seed location: S1


DTI

Overview of Pipeline

1

Rigid Registration

Individual cases are aligned to an external template atlas and the DTI metrics are computed from the raw DWI image


2

Skull Stripping

All non-brain tissue is removed from the image


3

Population Average Creation

The registered images are averaged together to create an image that is representative of the population of data.


4

Population Average Segmentation

The segmentation from the external template atlas is applied to the population atlas


5

Segmentation Propagation

The segmentation from the population average image is propagated, or warped back to the individual subjects.


6

Region Based Statistics

Both volume and diffusion based-metrics (FA, MD, AD, RD) can be gathered from the indvidual cases’ warped segmentation.


Sample Figures

Average Image of Colored FA

 

Average Image of MD, AD, RD

 

3D Images with ROIs

 

Average Image with 20 ROIs / Bar graphs and correlation plots