CBU default imaging sequences

Introductory note

The sequences shown on this page are meant to be used as guidelines, but they can be modified in order to meet the needs of your study. If you would like some advice on setting up your sequence, please contact Marta Correia ( marta.correia@mrc-cbu.cam.ac.uk ).

If you want to double check what parameters were used for images already acquired, you can also look at the information from the DICOM headers, which SPM saves when converting to Nifti format. After DICOM conversion every folder has a dicom_headers.mat file. In Matlab:

>> load dicom_headers.mat >> DICOMHEADERS{1}

will let you check the parameters for the images you've acquired.

CBU_EPI

For fMRI

Description

Standard EPI sequence for fMRI

Acquisition time

2 s (per volume)

Type

2D

Slices

32

Slice gap

25%

Slice thickness

3 mm

Slice order

Descending (32,31,...,1)

FOV

192 mm x 192 mm

Matrix

64 x 64

Resolution

3 mm x 3mm

TR

2000 ms

TE

30 ms

Flip angle

78 deg

Bandwidth

2232 Hz/Px

Echo spacing

0.51 ms

Trigger pulse timing

To within a few ms, the stimulus delivery trigger pulse happens 35 ms before the acquisition of the first scan (centre of k space) of each volume. Note there is a latency of 20 ms in the visual display. The trigger pulse length is 1 ms.

CBU_MEPI

The multi-echo sequence was developed by Benedikt Poser and colleagues at the FC Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands. A comparison between multi-echo and standard fMRI acquisition can be found here http://onlinelibrary.wiley.com/doi/10.1002/mrm.20900/pdf .

Description

Echo planar imaging at multiple echo times

Acquisition time

2.47s (per volume)

Type

2D

Slice

32

Slice gap

25%

Slice thickness

3mm

Slice order

Descending (32,31,...,1)

FOV

192mm x 192mm

Matrix

64 x 64

Resolution

3mm x 3mm

TR

2470ms

TE

9.4ms, 21.2ms, 33ms, 45ms, 57ms

Flip angle

83 deg

Parallel imaging

GRAPPA
Acceleration factor PE: 3
Reference lines PE: 24

CBU_MultiBand_EPI

CBU_MPRAGE

Description

High-resolution structural MRI

Acquisition time

4 min 32s

Type

3D

FOV

256 mm x 240 mm x 192mm

Matrix

256 x 240 x192

Resolution

1 mm isotropic

TR

2250 ms

TI

900 ms

TE

2.99 ms

Flip angle

9 deg

Parallel imaging

GRAPPA
Acceleration factor PE: 2
Reference lines PE: 24

CBU_T2

Description

High-resolution T2-weighted structural MRI

Acquisition time

4 min 30s

Type

3D

FOV

256 mm x 240 mm x 192mm

Matrix

256 x 240 x192

Resolution

1 mm isotropic

TR

2800 ms

TE

408 ms

Flip angle

90 deg

Bandwidth

751 Hz/Px

Echo spacing

3.36 ms

Parallel imaging

GRAPPA
Acceleration factor PE: 2
Reference lines PE: 24

CBU_TSE

Description

T2-weighted structural MRI

Acquisition time

1 min 38 s

Slices

29

Slice gap

30%

Slice thickness

4 mm

Type

2D

FOV

220 mm x 220 mm

Matrix

320 x 320

Resolution

0.7 x 0.7 mm

TR

5060 ms

TE

102 ms

Flip angle (refoc. pulse)

140 deg

Parallel imaging

GRAPPA
Acceleration factor PE: 2
Reference lines PE: 26

CBU_Fieldmapping

Description

Magnetic field mapping sequence. Required for
- undistortion of fMRI data
- functional sensitivity mapping

Acquisition time

54 s

Type

2D

Slices

32

Slice gap

25%

Slice thickness

3 mm

FOV

192 mm x 192 mm

Matrix

64 x 64

Resolution

3 mm x 3 mm

TR

400 ms

TE

5.19 ms / 7.65 ms

Flip angle

60 deg

CBU_DTI_InLea_2x2x2

Description

Standard sequence for diffusion MRI.
- isotropic voxel resolution
- interleaved slice acquisition

Acquisition time

8min 52s / 9min 33s

Type

2D

Slices

63 / 68

Slice gap

none

Slice thickness

2 mm

Slice order

Interleaved

FOV

192 mm x 192 mm

Matrix

96 x 96

Resolution

2 mm x 2 mm

TR

7800 ms / 8400 ms

TE

90 ms

Diff directions

64

Diff weightings

2

b-value1

0 s/mm2

b-value2

1000 s/mm2

Parallel imaging

GRAPPA
Acceleration factor PE: 2
Reference lines PE: 40

For more information on the diffusion MRI sequence go to AnalyzingDiffusion. If you have an ongoing study or wish to compare your results with data that you had previously acquired, the old standard CBU sequence for diffusion imaging (CBU_DTI_64D_1A) will still be available to be used.

CBU_SWI

Description

Susceptibility Weighted Imaging to image vessels and veins in the brain

Acquisition time

6min 38s

Type

3D

Slices

72

Slice gap

0%

Slice thickness

1.2 mm

Slice order

Interleaved

FOV

230mm x 178mm

Matrix

448 x 381

Resolution

0.6 mm x 0.5 mm

TR

28 ms

TE

20 ms

Flip angle

15 deg

Bandwidth

120 Hz/Px