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Data Processing for Analyzing Resting State fMRI written in Python

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Analyzing Resting State fMRI of Mice

Written in Python3 on Jupyter Notebook

Striatum In Rat

The Striatum is a nucleus cluster in the subcortical basa ganglia of the forbrain. It is a critical component of the motor and rewards system and coordinates multiple aspects of cognition including action planning, decision making, reward perception, etc. The striatum is divided into ventral and dorsal subdivisions. The ventral straitum is composed of the nucleus accumbens and the olfactory tubercle. The dorsal striatum is composed of caudate nucleus and the putamen. The striatum, especially the ventral striatum mediates reward cognition. reinforcement, and motivational salience whereas the dorsal striatum mediates motor funcctions, certain executive functions and stimulus response learning.

Fundamental Mechanism of fMRI

Functional magnetic resonance imaging, or fMRI works on the principle that certain isotopes of abundant elements in the human body exhibits a spin. This is measured in units using Plank’s constant and is a measure of the angular momentum of the nucleus. This spin gives the isotope a magnetic field which aligns itself in parallel to an applied magnetic field such as that of strong magnets in fMIR machines. When aligned with the magnetic field, the isotope is analogous to a gyroscope hanging from a vertical pivot in the magnetic field. When disturbed by an outside force, the gyroscope would wobble or ”precess” about the vertical axis. The time that the gyroscope takes to return back to its position is what creates the signal which builds into images. Coupled with magnetic field gradients and fourier transforms, fMRI creates a non invasive tool for imaging body functions.

Linear Regression and generation images

Regression Analysis and ICA Function

(Currently updating)

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