Pre-processing of MR images

Initially all 3D data (NIFTI format) of the brain MR images collected from the ADNI database were converted into 2D slices for the ease of handling the images and further pre-processing of the images. 2D images saved in DICOM format were converted into JPEG format. An in-house code was written to perform NIFTI/DICOM to JPEG conversion of the MR images. In this case different functions, [dicomread(), dicominfo(), and rgb2gray()], of MATLAB Image Processing Toolbox [56] have been used. dicomread() reads the image data of the dicom files. dicominfo() reads the metadata of the dicom file. rgb2gray() converts the RGB image to grayscale image.

Since quality of data is subjected to the efficiency of the operator and flexibility of the head of the subject, the orientation of brain substructures differs in subjects. Hence, this variation of orientation of the brain images needs to be adjusted and normalized with respect to fix reference frame. We oriented the images that seemed to be inclined due to image collection variations.

The following formula and corresponding rotation matrix were used to rotate the image at an angle, θ toward positive direction of x-axis assuming the centroid at the center of rotation

where, (x′, y′) is the new coordinates of a pixel whose current coordinate is (x,y)