MRI acuiqisition for beyond DTI analysis

Key parameters


1. Decide which resolution to use (2.5 mm, 2 mm, 1.5 mm), avoid none-isotropic resolution

    Higher resolution will reduce SNR and limited the highest applicable b-value. 

2. Decide b-value and b-table

    Multishell: Most applicable to every methods, but how to optimize shell sampling is still a challenge.

    Grid: Able to capture all diffusion pattern, but cannot be used by shell-based methods.

3. Decide phase encoding directions (AP, LR, SI)

    AP-PA: Most popular approach, but compressed voxels at frontal lobe and temporal lobe

    LR-RL: Least compressed voxels, but the brain shape becomes asymmetric. Data cannot be used without distortion correction.

    SI-IS: Need to flip the slices. 

4. Full opposite phase encoding or just b0

    B0 opposite phase encoding: Cannot use DSI Studio's distortion correction routine. Cannot recover compressed voxels

    Full opposite phase encoding: x2 scanning time

5. Decide monopolar or bipolar gradient 

    Monopolar: you cannot acquire high b-value image (e.g. > 4000) due to limited SNR for correcting the distortion

    Bipolar: Longer TE means lower SNR and greater susceptibility artifact.


Setting up b-table (diffusion sampling scheme)


The diffusion-weighted images can be acquired with a variety of combinations of gradient sensitization settings (schemes). The classification is often based on the spatial distribution of gradient encoding vectors (Gx,Gy,Gz).


Single-shell

(Gx,Gy,Gz) distributes equally on a sphere, where |G| is constant. It is noteworthy that there is no perfect tessellation of a unit sphere (except icosahedron), and thus it is impossible to keep sampling vectors perfectly equal distributed. Certain vectors will be closer to each other, causing bias. A sampling number ~100 or more in a shell is considered "high angular resolution".

Multi-shell

A combination of more than two single shells is termed multi-shell. Multi-shell scheme shares the same distribution problem as the single shell. In addition, the distance between shell points can be highly nonuniform and add more bias into the scheme.

Grid

The most popular non-shell scheme is the grid scheme, which is used by q-space imaging and diffusion spectrum imaging (DSI). (Gx,Gy,Gz) distributes on the Cartesian points within a sphere, where |G| is less than a maximum magnitude value. The major advantage of a grid scheme is its equal distance between sampling points. The limitation is that not every modeling method can work on grid sampling data. 

Others 
body-center-cubic and face-center-cubic.

How to choose a b-table?

Single shell maximizes the sensitive to orientation, whereas the grid scheme is a balance between orientation and radial information. The choice is thus depending on the application. If the study concerns only axonal direction, then the single shell is the most efficient approach. If the study involves pathological condition, then grid scheme gives the best coverage of both orientation and radial information.

Questions

1. Can we acquire multishell using existing DTI protocol?
2. Can we reconstruct DTI, HARDI, multishell, DSI data by DTI, ball-stick-model, CSD, NODDI, DSI, GQI? Why or why not?


Exercise
1. Load the sample images provided from Sample Images. Could you tell what diffusion scheme was used by the b-table?

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