RodentMRI-pipeline

Introduction

An open source and easy MRI processing pipeline for rodent (mouse & rat) sMRI, rfMRI and dMRI analysis.

Currently, only Mouse RfMRI pipeline is released. More is coming. Thank you for your support.

Getting Started

Prerequisites

1. Use a Linux or Mac environment

2. Install MRI toolboxes below by terminal (recommend to use conda):

   • FSL - FMRIB Software Library
   • ANTs - Advanced Normalization Tools

3. Install MATLAB, and 'set path' -> 'add with subfolders' to add all toolboxs in Toolboxs/.

   BrainNetViewer_20191031 
   dcm2niix 
   GRETNA_ZZD_v2 
   Rat_toolbox 
   spm12
   

Running the Project

Mouse RfMRI Analysis (中文 & English)

Follow manual in Manuals/Mouse_RfMRI_Manual_chn.md or Manuals/Mouse_RfMRI_Manual_eng.md.

Contact

For questions or feedback, please contact [email protected] or post issues.