trungmaster5 / bids_fmri_analysis_nipype

Analysis pipeline for fMRI (and structural) images in BIDs format

BIDS_fMRI_analysis_nipype

Analysis pipeline for fMRI (and structural) images in BIDs format

This repository contains a series of processing pipelines for fMRI (and structural) dataset in BIDs format, in form jupyter notebooks. The pipelines are implemented in nipype and are adapted from the Michael Notter tutorial. The scripts were developed to analyze specific fMRI data colleted during a Motor Imagery Neurofeedback task, however they can be easily extended to other datasets in BIDs format. To be able to use these notebooks and adapt them to your own analysis, you need to have installed the dependencies necessary to use Nipype

The pipeline is organized in three modules:

1. fMRI_preprocessing.ipynb

Preprocessing pipeline of fMRI and structural scans including

1. Motion Correction
2. Slice timing Correction
3. Outliers detection
4. Coregistration with structural scan

2. fMRI_1st_Level.ipynb

Individual GLM analysis model definition and estimation. Normalization of obtained contrast on MNI template.

3. fMRI_2nd_Level.ipynb

Group GLM analysis (one sample T-test model) and examples of visualization.