fMRI-functional-Magnetic-Resonance-Imaging-Data-Processing-Manual

This manual is still being updated periodically. The preprocessing tools are AFNI, fMRIPrep, and XCP-D. Post-processing primarily utilizes Python.

Handbook: https://qiuyuyu3.github.io/fMRI-Data-Processing-Manual-on-HPC/

Overview Pipeline¶

Table of Contents¶

Task_based¶

00 fMRI Resource

01 Introduction to Linux, GACRAC, and AFNI

02 Reconstruction: Convert 2D images to 3D (anatomical) or 4D (functional)

03 Preprocessing & afni_proc.py

04 General Linear Regression & Experimental Design This section is still in development

05 Preprocessing Pipeline: convert DICOM to Nifiti, sswarper2 & afni_proc.py

06 Quality Control

07 Group Analysis This section is still in development

Resting State¶

fMRI Prep, XCP-D, MRIQC, and Resting State fMRI

Functional Connectivity and Graph Theory This section is still in development

Other¶

Bias Field Correction (EPI distortion Correction)

Special Issues

Freesurfer and SUMA This section is still in development

Independent Component Analysis (ICA)