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