black0017 / medical_image_DTI_MRI

Medical Image processing project DTI & T1-MRI

Medical Image processing project DTI & T1-MRI

Assignment Description

• After downloading, extracting and reading the nii, bval and bvec files:
  1. Calculate the coloured FA (fractional anisotropy) map of the exam using the dti files. Doing so is quite complex so it's recommended to use the dipy.reconst.dti module of the dipy python library.
  2. Transform the coordinate space of the coloured FA map onto the coordinate space of the T1 sequence using the information taken from the affine headers of the nifti files. In order to do this, you MUST use scipy.ndimage.affine_transform.
  3. Generate png images for the middle axial, coronal and sagittal slices, displaying the grayscale T1 sequence with the coloured FA map semi-transparently superimposed on top of it. In order to do this, you MUST use PIL.Image.

Instructions

To reproduce the code:

1. open the terminal in the project directory
2. run the following command: sudo docker build -t enviroment:latest .
3. to make sure the docker image is created run: docker images
4. run in sudo mode: docker run -it enviroment
5. run the command: python3 script.py
6. results will be produced in the data folder

Note: for the generated png images: ‘x’ - sagittal, ‘y’ - coronal, ‘z’ - axial views.