ImagingSequences - MRC CBU Imaging Wiki
location: ImagingSequences

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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 ).

Here NewSequences.ppt you can find an overview of the sequences which have recently been implemented in our scanner.

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_SilentEPI

Schmitter et al, Magn Reson Mater Phy (2008) 21:317–325.

Peelle JE, Eason RJ, Schmitter S, Schwarzbauer C, Davis MH (2010) Evaluating an acoustically quiet EPI sequence for use in fMRI studies of speech and auditory processing. NeuroImage. http://dx.doi.org/10.1016/j.neuroimage.2010.05.015

See UsingTheSilentSequence for discussion.

Description

Quiet echo-planar imaging for auditory FMRI

Acquisition time

2.64s (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

2640 ms

TE

44 ms

Flip angle

83 deg

Bandwidth

1220 Hz/Px

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_3DEPI

Description

3D fast imaging sequence for high resolution fMRI

Acquisition time

1.508 s / 1.060 s / 1.326 s (per volume)

Type

3D

Slices

40 / 30 / 20

Slice gap

0%

Slice thickness

1.5mm / 2mm / 3mm

FOV

192 mm x 192 mm

Matrix

192x192 / 128x128 / 96x96

Resolution

1.5mmx1.5mm / 2mmx2mm / 3mmx3mm

TR

58 ms / 53 ms / 51 ms

TE

30 ms

Flip angle

16 deg / 15 deg / 15 deg

Bandwidth

1628 / 2228 / 2228 Hz/Px

Parallel imaging

GRAPPA
Acceleration factor PE: 2x2
Reference lines PE: 40x40

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

MGH_MEMPRAGE

This multi-echo MPRAGE sequence has been optimised for use with FreeSurfer (more information can be found here http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&do=get&target=FreeSurfer_Suggested_Morphometry_Protocols.pdf). The advantages of this sequence are also discussed in this paper http://www.ncbi.nlm.nih.gov/pubmed/18242102.

This sequence is recommended for morphometry studies where time is limited, in particular if cortical thickness or cortical thickness and segmentation of other brain structures is the main interest.

This is not a Siemens product sequence and consequently there are restrictions on its use, so please contact Marta Correia ( marta.correia@mrc-cbu.cam.ac.uk ) if you'd like more information on this sequence.

Description

Multi-echo high resolution structural MRI (4 echoes)

Acquisition time

6min 3s

Type

3D

FOV

256 mm x 256mm x 192mm

Matrix

256 x 256 x 192

Resolution

1 mm isotropic

TR

2530 ms

TI

1200 ms

TE

1.64 , 3.5 , 5.36 , 7.22 ms

Flip angle

7 deg

Bandwidth

651 Hz/Px

Parallel imaging

GRAPPA
Acceleration factor PE: 2
Reference lines PE: 32

MGH_MEFLASH

This FLASH protocol is recommended for whole-brain segmentation where all brain structures are labeled by FreeSurfer. The acquisition requires more time – at least two separate acquisitions at two different flip angles are needed. Information on Multi-echo FLASH data analysis can be found here http://surfer.nmr.mgh.harvard.edu/fswiki/MEF .

This is not a Siemens product sequence and consequently there are restrictions on its use, so please contact Marta Correia ( marta.correia@mrc-cbu.cam.ac.uk ) if you'd like more information on this sequence.

Description

Multi-echo FLASH sequence for whole brain morphometry

Acquisition time

8min 28s per flip angle acquisition (minimum 16min 56s)

Type

3D

FOV

256 mm x 256mm x 192mm

Matrix

256 x 256 x 192

Resolution

1 mm isotropic

TR

20 ms

TE

1.85 + n*2.0 ms (n = 0,..,7)

Flip angle

5 and 30 deg (then 20, then 3 degrees)

Bandwidth

651 Hz/Px

Parallel imaging

GRAPPA
Acceleration factor PE: 2
Reference lines PE: 32

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_GQI_101

Description

High angular resolution diffusion MRI sequence for GQI analysis

Acquisition time

14min 21s

Type

2D

Slices

55

Slice gap

none

Slice thickness

2.5 mm

Slice order

Interleaved

FOV

240mm x 240mm

Matrix

96 x 96

Resolution

2.5 mm x 2.5 mm

TR

8200 ms

TE

69 ms

Diff directions

101

Diff weightings

multiple

max b-value

4000 s/mm2

flip angle

90 deg

Bandwidth

2004 Hz/Px

Parallel imaging

GRAPPA
Acceleration factor PE: 3
Reference lines PE: 40

CBU_MTI

Description

Magnetization Transfer Imaging

Acquisition time

2 x 2min 36s

Type

3D

Slices

84

Slice gap

0%

Slice thickness

1.5 mm

Slice order

Interleaved

FOV

192 mm x 192 mm

Matrix

128 x 128

Resolution

1.5 mm x 1.5mm

TR

30 ms

TE

5 ms

Flip angle

12 deg

Bandwidth

190 Hz/Px

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

CbuImaging: ImagingSequences (last edited 2013-03-07 21:23:50 by localhost)