T1w_Preprocess

This is a basic pipeline to preprocess T1-weighted (T1w) Structural MRIs for visualization and further processing. This tool is designed for command-line use.

Overview

The preprocessing pipeline includes four primary steps:

1. Reorientation - Aligning the MRI images to a standard orientation.
2. Skull Stripping - Removing non-brain tissues from the MRI images.
3. Bias Correction - Correcting intensity non-uniformities in the MRI images.
4. Registration - Aligning an atlas to the patient space for standardized anatomical referencing.

Features

• Written primarily in Python.
• Utilizes the Nipype library for workflow management.
• Employs tools such as FSL and ANTs for processing tasks.
• Compatible with the Brain Imaging Data Structure (BIDS) Standard.

Inputs and Outputs

Inputs

At minimum:

• Parent Data Directory: The directory containing the MRI data.
• Subject ID: Identifier for the subject/patient.
• Output Directory: Directory where the processed outputs will be saved.

Outputs

1. Preprocessed Patient T1 MRI: The MRI after all preprocessing steps.
2. Atlas in Patient Space: An atlas registered to the patient’s anatomical space.

Usage

To use this tool, run the command:

python3 t1_preproc.py -p [data_dir_path] -sid [subject-id] -o [output_path]

Development Status

This tool is a work in progress. It is currently fully functional but is undergoing refinement to enhance user flexibility and input handling.

Feedback and Contributions

If you have any concerns or suggestions regarding the code or its implementation, please contact the authors at [email protected].