1. fMRI data acquisition

2. Prescribing the slices
Number of slices
Orientation
Thickness
Inplane resolution
Coverage

3. Inplane anatomical slices T1 weighted images
Top
Inplane anatomical slices
T1 weighted images
Front
Back
Bottom

4. Prescribing
Acquisition parameters

5. Inplane functional slices T2* weighted images
Top
Inplane functional slices
T2* weighted images
Front
Back
Bottom

6. What is the best way to acquire data?
The effect of scanning parameters
Parameters that affect signal-to-noise:
TE: echo time
Flip angle
Parameters that effect resolution:
TR – repetition time
FOV – field of view
Matrix size

7. What is the best way to acquire data?
The effect of scanning parameters
Parameters that affect signal-to-noise:
TE – echo time
Flip angle
Parameters that affect resolution:
TR – repetition time
FOV – field of view
Matrix size
Number of slices
Slice thickness

8. Prescribing
Acquisition parameters

9. Temporal parameters
TE: echo time

10. Temporal parameters
TE: echo time
TR: repetition time

11. Two factors that determine the time in which MRI images are collected
Echo Time (TE) is the time interval between the excitation RF pulse and data acquisition
Ranges of TE [msec]
Depends on pulse sequence and T2 parameters of tissue
Consult with your physicist
For T2* weighted images the amount of signal loss depends on the time of excitation and data acquisition or echo time. There is an optimal combination of TE and TR that maximizes the T2* of a tissue
If TE is very short, there is not much transverse magnetization loss and there is no T2* contrast
If TE is very long, the too much of the transverse magnetization will be lost and again there sill be no T2* contrast
Typically in fMRI researchers use the shortest TE possible.
(generally want long TR and short TE); long TR will enable Longitudinal magnetization to recover and thus most of our signal is from the transverse magenetization (or T2 weighted)
BOLD relies on T2* weighted imaging because we want to capture the local inhomogeneities produced by the deoxy-hemoglobin

12. Two factors that determine the time in which MRI images are collected
Echo Time (TE) is the time interval between the excitation RF pulse and data acquisition
Ranges of TE [msec]
Depends on pulse sequence and T2 parameters of tissue
Consult with your physicist
Repetition Time (TR) is the time interval between successive excitation pulses
Ranges of TR times used 500[msec] - 4[sec];
Trade off between number of slices, inplane resolution, and TR
Longer TRs may be needed for higher spatial resolution and more slices

13. Two factors that determine the time in which MRI images are collected
Echo Time (TE) is the time interval between the excitation RF pulse and data acquisition
Ranges of TE [msec]
Depends on pulse sequence and T2 parameters of tissue
Consult with your physicist
Repetition Time (TR) is the time interval between successive excitation pulses
Ranges of TR times used 500[msec] - 4[sec];
Trade off between number of slices, inplane resolution, and TR
Longer TRs may be needed for higher spatial resolution and more slices
Multiplexing (MUX) algorithms using acquisition from multiple parallel coils enable whole brain acquisition (48 slices) at a 1 second TR, without much comprimising the signal-to-noise

14. Flip Angle
Ranges for the flip angle 0-90°

15. Flip Angle
The Ernst angle (or flip angle) is the angle the gradient is applied for a particular spin to give the maximal signal in the minimal time.
This relationship was development by Richard Ernst winner of the 1991 Nobel Prize in Chemistry.

16. Calculating the Flip Angle
The best signal to noise ratio in gradient echo scans (EPI or otherwise) is achieved with a flip angle equal to the so-called Ernst angle:
T1 is the longitudinal relaxation time of the object you are imaging.
TR is the repetition time

17. Calculating the Flip Angle
The best signal to noise ratio in gradient echo scans (EPI or otherwise) is achieved with a flip angle equal to the so-called Ernst angle:
T1 is the longitudinal relaxation time of the object you are imaging.
TR is the repetition time
T1 of the gray matter at 3T is about 1400 msec.
T1 of white matter is about 830 msec
(Wansapura et al, J Mag Resonance Imaging, 1999).

18. Calculating the Flip Angle
The best signal to noise ratio in gradient echo scans (EPI or otherwise) is achieved with a flip angle equal to the so-called Ernst angle:
T1 is the longitudinal relaxation time of the object you are imaging.
TR is the repetition time
T1 of the gray matter at 3T is about 1400 msec.
T1 of white matter is about 830 msec
(Wansapura et al, J Mag Resonance Imaging, 1999).
Example:
T1=1400 [msec]; TR=2000 [msec];
 = acos(exp(-TR/T1)) = [rad]=76.1[°]

19. Calculating the Flip Angle
The best signal to noise ratio in gradient echo scans (EPI or otherwise) is achieved with a flip angle equal to the so-called Ernst angle:
T1 is the longitudinal relaxation time of the object you are imaging.
TR is the repetition time
T1 of the gray matter at 3T is about 1400 msec.
T1 of white matter is about 830 msec
(Wansapura et al, J Mag Resonance Imaging, 1999).
Example:
T1=1400 [msec]; TR=2000 [msec];
 = acos(exp(-TR/T1)) = [rad]=76.1[°]

20. Relationship between TR & Flip Angle
Note that the shorter the TR, the more the improvement to be gained with smaller flip angles.

21. Parameters that affect spatial resolution
Number of slices

22. Parameters that affect spatial resolution
Number of slices
Slice thickness

23. Parameters that affect spatial resolution
Number of slices
Slice thickness
FOV – field of view

24. Parameters that affect spatial resolution
Number of slices
Slice thickness
FOV – field of view
Matrix size

25. Parameters that determine MRI resolution
Field of View (FOV): the spatial extent along a dimension in image space
Typical FOV: 192mm-240mm
Depends on the orientation which you slice the brain, e.g. coronals require smaller FOV than axials.
Need to leave air outside brain to avoid aliasing

26. Parameters that determine MRI resolution
Field of View (FOV): the spatial extent along a dimension in image space
Typical FOV: 192mm-240mm
Depends on the orientation which you slice the brain, e.g. coronals require smaller FOV than axials.
Need to leave air outside brain to avoid aliasing
Matrix size: Determines the number of samples in k-space.
Typical matrix size: 64; high resolution may use a matrix size of 80, 100, or 128.
Usually a power of 2 because the way the Fourier transform is implemented digitally.
Increasing the matrix size requires consultation with a physicist and affects TR as it affect slice readout time

27. Parameters that determine MRI resolution

28. Parameters that determine fMRI resolution

29. Parameters that determine MRI resolution

30. Prescribing
Acquisition parameters