MRI Scripts

This repository contains scripts for processing and analyzing MRI data, focusing on DTI and fMRI analysis. The scripts are designed to extract brain imaging features such as Mean Diffusivity (MD) and Fractional Anisotropy (FA) for DTI, and ROI activation for task-based fMRI.

Setup and Dependencies

Ensure you have the necessary software for processing DTI and fMRI data, including:

• FSL (for TBSS and fMRI processing)
• Python (for any auxiliary processing)
• Additional MRI toolboxes as required

DTI Analysis

1. Place your DTI data in the appropriate directory.

2. Run the extract_task_ROI_activation.sh script in the DTI folder to extract the Mean Diffusivity (MD) and Fractional Anisotropy (FA) values for the regions specified:

   • Uncinate Fasciculus
   • Cingulum

   These regions can be updated to match your specific areas of interest by modifying the script.

fMRI ROI Extraction

1. Place your task-based fMRI data in the appropriate directory.
2. Run the script in the fMRI folder to extract activation data from the designated Regions of Interest (ROIs).

Notes

• DTI Analysis:
  The current script is set to extract MD and FA values from the Uncinate Fasciculus and Cingulum. Users can modify the regions of interest (ROIs) as necessary by editing the script.

• Atlas Files:
  The atlas files:

  • JHU-ICBM-labels-2mm.nii.gz
  • MNI152_T1_2mm.nii.gz

  These are required for alignment and ROI extraction. Ensure that these files are in the correct format and resolution for your data.

• fMRI Analysis:
  The script in the fMRI folder is designed for task-based fMRI analysis. Modifications may be required for different tasks or research goals.

Contributing

Feel free to fork this repository, make modifications, and submit pull requests. Contributions are welcome!

License

This repository is licensed under the MIT License - see the LICENSE file for details.