Sequences

Introductory note

The default MRI 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 MR Physics (###).

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 you can check the parameters for the images you've acquired:

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

BCAN_fMRI

Description

Standard EPI sequence for fMRI

Acquisition time

2000 ms (per volume)

Type

2D

Slices

33

Slice gap

25%

Slice thickness

3 mm

Slice order

Descending (33,32,...,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

For accurate slice time correction consider this document. See also here and here.

The Siemens system includes additional "dummy scans" at the beginning of the acquisition to allow the magnetization to stabilize to a steady state. The dummy scans are not stored, so they will make the banging sound like normal scans but there will be no data associated with them. There will be a trigger pulse that occurs with the first REAL SCAN (i.e. after the last dummy scan). The number of dummy scans is chosen to guarantee more than 3 seconds of time for stabilization: Dummy scans = ROUNDUP(3001/TR), e.g.
  • If the number of "measurements" is 1 then there are NO DUMMY SCANS
  • TR > = 3001ms: 1 dummy scan
  • 3001 < TR <= 1501ms: 2 dummy scans
  • 1501 < TR <= 1001ms: 3 dummy scans

BCAN_Fieldmap

Description

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

Acquisition time

54 s

Type

2D

Slices

33

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

The phase encoding direction of the BCAN_fMRI sequence to be undistorted is A>>P.


readOutTime = echoSpacing * ((matrixLines*partialFourier/accelerationFactor)-1)

More about undistortion and statistical power here

 

BCAN_Resting

Description

Standard EPI sequence for fMRI

Acquisition time

2000 ms (per volume)

Type

2D

Slices

33

Slice gap

20%

Slice thickness

3 mm

Slice order

Descending (33,32,...,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

For accurate slice time correction consider this document.

BCAN_MPRAGE

Description

High-resolution structural MRI

Acquisition time

4 min 26s

Type

3D

FOV

256 mm x 256 mm x 192mm

Matrix

256 x 256 x192

Resolution

1 mm isotropic

TR

1900 ms

TI

900 ms

TE

2.52 ms

Flip angle

9 deg

Parallel imaging

GRAPPA 
Acceleration factor PE: 2 
Reference lines PE: 24


BCAN_DTI

Description

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

Acquisition time

8min 32s

Type

2D

Slices

61

Slice gap

none

Slice thickness

2.3 mm

Slice order

Interleaved

FOV

220 mm x 220 mm

Matrix

96 x 96

Resolution

2.3 mm x 2.3 mm

TR

7500 ms

TE

86 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: 28


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