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+# Preprocessing on Brain MRI Sequence
+
+This is a pipeline to do preprocessing on brain MR images of **ADNI** dataset  
+by using FMRIB Software Library (**FSL**) and Advanced Normalization Tools (**ANTs**).
+
+## 1. Install FSL & ANTs
+
+Download and install **FSL** as instructions [here](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation).  
+Compile **ANTs** from source code in [Linux and macOS](https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS), or in [Windows 10](https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Windows-10).
+
+## 2. Install Python Packages
+
+All required libraries are listed as below:
+
+- tqdm
+- numpy
+- scipy
+- nipype
+- nibabel
+- matplotlib
+- sciKit-fuzzy (optional)
+- scikit-learn (optional)
+
+## 3. Download Dataset
+
+The dataset used in this repo is AD and NC screening images of ADNI1 and ADNI2.  
+See [README.md in *data*](https://github.com/quqixun/BrainPrep/tree/master/data).
+
+Here is one sample of original image.  
+
+<img src="https://github.com/quqixun/BrainPrep/blob/master/imgs/original.png" alt="original image" width="250">
+
+## 4. Reorgnization Files
+
+Switch the working directory to *src*.
+Run reorgnize.py, which merge ADNI1 and ADNI2 into one folder.
+```
+python reorgnize.py
+```
+
+## 5. Registration
+
+Run registraion.py to transform images into the coordinate system of template by **FSL FLIRT**.
+```
+python registraion.py
+```
+
+The output of the above image from this step looks like:  
+
+<img src="https://github.com/quqixun/BrainPrep/blob/master/imgs/registration.png" alt="registration" width="250">
+
+## 6. Skull-Strpping
+
+Run skull_stripping.py to remove skull from registrated images by **FSL BET**.
+```
+python skull_stripping.py
+```
+
+ Output:  
+ 
+<img src="https://github.com/quqixun/BrainPrep/blob/master/imgs/skull_stripping.png" alt="skull stripping" width="250">
+
+## 7. Bias Field Correction
+
+Run bias_correction.py to remove bias-field signal from images by **ANTs**.
+```
+python bias_correction.py
+```
+
+Output:
+
+<img src="https://github.com/quqixun/BrainPrep/blob/master/imgs/bias_correction.png" alt="bias field correction" width="250">
+
+## 8. Enhancement (optional)
+
+Based on outputs from step 7, run enhancement.py to enhance images by **histogram equalization**.
+```
+python enahncement.py
+```
+
+## 9. Tissue Segmentation (optional)
+
+Based on outputs from step 7, run segment.py to segment brain into GM, WM and CSF  
+by **KMeans** or **Fuzzy-CMeans** (you should change settings in script).
+```
+python segment.py
+```
+Or run fast_segment.py to do segmentation by **FSL FAST**.
+```
+python fast_segment.py
+```