Abstract

Introduction

Methods

Participants

Data for this study is from a subset of individuals who participated in the European DTI Study on Dementia \cite{Brueggen2017}, a multi-center study which included patients diagnosed with either Alzheimer's Disease (AD) or mild cognitive impairment (MCI), as well as healthy controls (HC). The data included here consists of neuroimages and measures of cognitive impairment from 26  such individuals--10 (8 female, 2 male), ages 63-85 (avg. = 75.1 yrs., SD = 6.69), diagnosed with  AD, and 16 (9 female, 7 male) healthy controls, ages 53-72 (avg. =  64.38 yrs., SD = 6.11). 

MRI Acquisitions

The MRI data were acquired using a 3T Siemens TIM-Trio (Siemens Medical Inc., Erlangen, Germany). Scans included T1-weighted structural images and T2 diffusion-weighted images (DWI).

T1 Scan Parameters

The scan parameters for the T1 images were: TR (Repetition Time) = 2200 ms, TE (Echo Time) = 2.2 ms, flip angle = 12 degree, and  1 x 1 x 1 mm3 resolution.

DWI Scan Parameters

The DWI scan parameters were:  61 gradient directions, b-Values=1000, TR=11,800, TE=94, flip angle=90, and 2 x 2 x 2 mm3 resolution. 

T1 Preprocessing Steps

The initial images from the scanner were preprocessed to reduce or remove artifacts and confounds from the data. The preprocessing steps are as follows:

Convert the images from the DICOM file format to NifTi using dcm2niix (v1.0.2017821, Webiste download:  https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage)

There are two files to convert from DICOM to NifTi, the T1 structural image and the diffusion-weighted image (dwi). Input for each was the raw DICOM file, output is a NifTi file. The -f option indicates the file name for the output--t1 and dwi. The affirmative -x option indicates that the file will be cropped and reoriented; the "n" after the -z option indicates that the structural T1 file will not be compressed, whereas the "y" indicates that the T2 diffusion-weighted (DWI) will be compressed. There are two additional outputs for the DWI data besides the NIfTI files, a .bval file, a file containing b-values (the amount of diffusion weighting for each volume), and a .bvec file, a gradient diffusion table containing the b-vectors (the gradient directions).