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Standard sequences

These sequences are implemented and ready-to-use with theses parameters kindly shared by the MRC-CBSU in Cambridge, UK.

They can be used in most use cases; however, they can be also modified when required. Feel free to contact with Ari, Ayan for further guidance!

They are also stored in the DICOM headers if you want to double check before processing (recommended!).

  • In Linux, you can use mri_probedicom available in FreeSurfer:
    mri_probedicom --i <DICOM filename>
  • In MATLAB, you can use spm_dicom_headers available in SPM:
    hdr = spm_dicom_headers('<DICOM filename>');
    hdr{1}

MPRAGE

High resolution, T1-weighted, structural MRI

Parameter Value
Acquisition time 4 min 32 s
Type 3D (sagittal slices)
FOV (A-P x L-R x F-H) 256 mm x 192 mm x 256 mm
Matrix 256 x 256 x 192 (rotated!)
Resolution 1 mm isotropic
TR 2250 ms
TI 900 ms
TE 2.98 ms
Flip angle 9 deg
Parallel imaging GRAPPA
Acceleration factor PE: 2
Reference lines PE: 24

For Incidental Findings

TSE

Quick, high (in-plane) resolution, T2-weighted, structural MRI (for incidental findings)

Parameter Value
Acquisition time 1 min 38 s
Type 2D
Slices 29
Slice thickness 4 mm
Slice gap 30% (1.2 mm)
FOV 220 mm x 220 mm
Matrix 320 x 320
Resolution 0.7 mm x 0.7 mm
TR 5060 ms
TE 102 ms
Flip angle 140 deg
Parallel imaging GRAPPA
Acceleration factor PE: 2
Reference lines PE: 26

TSE_FLAIR

High (in-plane) resolution, T2-weighted, 'dark-fluid', structural MRI (for incidental findings)

Parameter Value
Acquisition time 4 min 32 s
Type 2D
Slices 25
Slice thickness 4 mm
Slice gap 30% (1.2 mm)
FOV 220 mm x 220 mm
Matrix 256 x 256
Resolution 0.9 mm x 0.9 mm
TR 9000 ms
TI 2500 ms
TE 100 ms
Flip angle 150 deg

T2*-weighted EPI sequences with BOLD contrast

Standard fMRI

Functional MRI with 3 mm isotropic spatial resolution

EPI_Standard

Standard fMRI, 2 s per volume

Parameter Value
Acquisition time 2 s (per volume)
Type 2D
Slices 32
Slice thickness 3 mm
Slice gap 25% (0.75 mm)
Slice order Descending (32 - 1)
FOV 192 mm x 192 mm
Matrix 64 x 64
Resolution 3 mm x 3 mm
TR 2000 ms
TE 30 ms
Flip angle 78 deg
Bandwidth 2112 Hz/Px
Echo spacing 0.54 ms

EPI_Standard_1s

Standard fMRI, 1 s per volume with reduced brain coverage

Parameter Value
Acquisition time 1 s (per volume)
Slices 16
Slice order Descending (16 - 1)
TR 1000 ms
Bandwidth 2232 Hz/Px
Echo spacing 0.51 ms

Other parameters are those of EPI_Standard.

High Resolution fMRI

Functional MRI with 2 mm isotropic or higher spatial resolution

EPI_HighRes_2iso

fMRI with 2 mm isotropic spatial resolution, 2 s per volume. Keep in mind that the thinner slices leads to reduced brain coverage!

Parameter Value
Acquisition time 2 s (per volume)
Type 2D
Slices 32
Slice thickness 2 mm
Slice gap 25% (0.5 mm)
Slice order Descending (32 - 1)
FOV 192 mm x 192 mm
Matrix 96 x 96
Resolution 2 mm x 2 mm
TR 2000 ms
TE 30 ms
Flip angle 78 deg
Bandwidth 1628 Hz/Px
Echo spacing 0.7 ms
Parallel imaging GRAPPA
Acceleration factor PE: 2
Reference lines PE: 48

EPI_HighRes_2iso_WholeBrain

fMRI with 2 mm isotropic spatial resolution, 40 slices for a whole brain coverage. Keep in mind that acquiring more slices leads to longer acquisition time!

Parameter Value
Acquisition time 2.5 s (per volume)
Slices 40
TR 2500 ms

Other parameters are those of EPI_HighRes_2iso.

EPI_HighRes_2iso_LargerFOV

fMRI with 2 mm isotropic spatial resolution, with a FOV of 205 mm for patricipants with larger head. Keep in mind that acquiring slices with larger FOV leads to slightly fewer slices thus slightly more reduced brain coverage!

Parameter Value
Slices 30
FOV 205 mm x 205 mm
Matrix 102 x 102
Bandwidth 1400 Hz/Px
Echo spacing 0.8 ms

Other parameters are those of EPI_HighRes_2iso.

EPI_HighRes_1.5x1.5x2mm

fMRI with 1.5 mm in-plane (highest achievable) spatial resolution, 2 s per volume. Keep in mind that acquiring slices with higher resolution leads to slightly fewer slices thus slightly more reduced brain coverage!

Parameter Value
Acquisition time 2 s (per volume)
Slices 28
Matrix 128 x 128
Resolution 1.5 mm x 1.5 mm
Bandwidth 1502 Hz/Px
Echo spacing 0.75 ms

Other parameters are those of EPI_HighRes_2iso.

Magnetic field mapping sequences required to

  • undistort EPI data (e.g. fMRI, DWI)
  • measure functional sensitivity

:!: It has to be acquired with the same geometry (FOV, resolution, alignment, slice centre) as the EPI data! :!:

Standard Fieldmap

Fieldmap with 3 mm isotropic spatial resolution. It matches with Standard fMRI sequences.

Fieldmapping

Dual-echo fieldmap

Parameter Value
Acquisition time 54 s
Type 2D
Slices 32
Slice thickness 3 mm
Slice gap 25% (0.75 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

High Resolution Fieldmaps

Fieldmaps 2 mm isotropic or higher spatial resolution. They match with High resolution fMRI sequences.

Fieldmapping_2iso

High resolution dual-echo fieldmap

Parameter Value
Acquisition time 1 m 19 s
Type 2D
Slices 32
Slice thickness 2 mm
Slice gap 25% (0.5 mm)
FOV 192 mm x 192 mm
Matrix 96 x 96
Resolution 2 mm x 2 mm
TR 400 ms
TE 5.19 ms, 7.65 ms
Flip angle 60 deg

Fieldmapping_2iso_WholeBrain

High resolution dual-echo fieldmap with whole brain coverage

Parameter Value
Acquisition time 1 m 26 s
Slices 40
TR 437 ms

Other parameters are those of Fieldmapping_2iso.

Fieldmapping_2iso_LargerFOV

High resolution dual-echo fieldmap with larger FOV

Parameter Value
Acquisition time 1 m 24 s
Slices 30
FOV 205 mm x 205 mm
Matrix 102 x 102

Other parameters are those of Fieldmapping_2iso.

Fieldmapping_1.5x1.5x2mm

High resolution dual-echo fieldmap with our highest achievable in-plane resolution

Parameter Value
Acquisition time 1 m 45 s
Slices 32
Matrix 128 x 128
Resolution 1.5 mm x 1.5 mm

Other parameters are those of Fieldmapping_2iso.


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