Brain_MR_Image_Preprocessing

Preprocessing pipeline of Brain MR Image for medical research.

*For installation of preprocessing tools and code usage, check out reference.md.

Update log

6/22
Code that applies brain mask added.

6/23
New variable T1C_label added.

7/6
New variable mask_label added.

7/7
'try-except' was added when finding T1Cpath and T2path using glob since the files might not exist.

8/4
Clean outputdir(MONSTR) before skull-stripping added.

Overview

Tools

1)ANTs(Advanced Normalization Tools)

• A tool for biomedical image analysis with a focus on registration, segmentation, etc.
• Used for Resampling, N4 Bias Correction, Co-registration.

2)MONSTR(Multi-cONtrast brain STRipping method )

• A software tool to generate brain masks (or skull-strip) from multi-contrast MR brain images, such as T1, T2, PD, or FLAIR.
• Compared to other tools that are validated on T1-based skull stripping methods, MONSTR involves multi-modal inputs(supports T1, T2, FLAIR)와 multi-model atlases.
• Used for Skull Stripping.

Step

1) Resampling

• Resize voxel to 1X1X1.
• Output

2) N4 Bias Correction

• Method for correcting low frequency intensity non-uniformity present in MRI image data known as a bias or gain field.
• Output

3) Co-Registration (to T1C)

• Brings one image(mostly T1C) to match another image, such that the same voxels refers roughly to the same structure in both brains.
• Output

4) Skull-Stripping + Apply skull mask

• Generate skull mask for each brain image, and strip.
• Output