Introduction to Neuroimaging

1. The quality of the measured data depends on the resolution and the following parameters:

   repetition time (TR): time required to scan one volume
   acquisition time (TA): time required to scan one slice. TA = TR - (TR/number of slices)
   field of view (FOV): defines the extent of a slice, e.g. 256mm x 256mm

2. Specifics of MRI Data

   For NifTI format, they are in the same file (.nii-file), whereas in the older Analyze format, they are in separate files (.img and .hdr-file).

   The image is the actual data and is represented by a 3D matrix that contains a value (e.g. gray value) for each voxel.
   The header contains information about the data like voxel dimension, voxel extend in each dimension, number of measured time points, a transformation matrix that places the 3D matrix from the image part in a 3D coordinate system, etc.

3.Modalities of MRI Data

sMRI (structural MRI)

    Structural magnetic resonance imaging (sMRI) is a technique for measuring the anatomy of the brain. By measuring the amount of water at a given location, sMRI is capable of acquiring a detailed anatomical picture of our brain. This allows us to accurately distinguish between different types of tissue, such as gray and white matter. Structural images are high-resolution images of the brain that are used as reference images for multiple purposes, such as corregistration, normalization, segmentation, and surface reconstruction.

    As there is no time pressure during acquisition of anatomical images (the anatomy is not supposed to change while the person is in the scanner), a higher resolution can be used for recording anatomical images, with a voxel extent of 0.2 to 1.5mm, depending on the strength of the magnetic field in the scanner, e.g. 1.5T, 3T or 7T. Grey matter structures are seen in dark, and the white matter structures in bright colors.

fMRI (functional MRI)
Functional magnetic resonance imaging (fMRI) is a technique for measuring brain activity.
Functional magnetic resonance imaging (fMRI) is a technique for measuring brain activity. It works by detecting the changes in blood oxygenation and blood flow that occur in response to neural activity.
Depending on the paradigm, we talk about event-related, block or resting-state designs.

event-related design: Event-related means that stimuli are administered to the subjects in the scanner for a short period. The stimuli are only administered briefly and generally in random order. Stimuli are typically visual, but audible or or other sensible stimuli could also be used. This means that the BOLD response consists of short bursts of activity, which should manifest as peaks, and should look more or less like the line shown in the graph above.
block design: If multiple stimuli of a similar nature are shown in a block, or phase, of 10-30 seconds, that is a block design. Such a design has the advantages that the peak in the BOLD signal is not just attained for a short period but elevated for a longer time, creating a plateau in the graph. This makes it easier to detect an underlying activation increase.
resting-state design: Resting-state designs acquire data in the absence of stimulation. Subjects are asked to lay still and rest in the scanner without falling asleep. The goal of such a scan is to record brain activation in the absence of an external task. This is sometimes done to analyze the functional connectivity of the brain.

dMRI (diffusion MRI)
Diffusion imaging is done to obtain information about the brain’s white matter connections. There are multiple modalities to record diffusion images, such as diffusion tensor imaging (DTI), diffusion spectrum imaging (DSI), diffusion weighted imaging (DWI) and diffusion functional MRI (DfMRI).
相关链接：miykael.github.io/nipype-beginner-s-guide/neuroimaging.html#fmri-functional-mri