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}
Structural
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 |
BOLD fMRI
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.
Fieldmap
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.