Introductory noteThe 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_fMRIDescription | 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_FieldmapDescription | 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_RestingDescription | 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_MPRAGEDescription | 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_DTIDescription | 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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