This page lists a few common and useful MRI sequences available on the 3T Trio. All of these scans use the 12-channel head coil. These are fairly generic protocols, and we can trade-off between resolution, scan time and signal to noise for individual studies, as demonstrated by our NewSeg protocols.
- Time per volume: 0:02.38
- Notes: Rapid functional scan for analysis with SPM or FSL. Alternatively, you may get a slightly better signal with a TE of 35ms (requiring a 2380ms TR). Go to the BOLD tab and set the ‘measurements’ to specify how many volumes you want to acquire.
- Protocol: This EPI scan uses a 90-degree flip angle, TE= 30ms, TR=2200ms, 64×64 matrix, 192×192mm FOV, 36 ascending 3mm thick slices with 20% slice gap (effectively 3×3x3.6mm between voxel centers), bandwidth 2232 Hz/px. For B0 unwarping, echo spacing is 0.51ms, phase encoding is A>P (”y-”).
Field Map (B0)
- Time per volume:0:54.
- Notes: Designed for FSL B0 undistortion – this image can be used to determine and correct for spatial distortion in the fMRI protocol. Use ”Copy Parameters” to collect an image with the same position and orientation as the fMRI sequence.
- Protocol: This Gradient Echo scan acquires two TEs (5.19 and 7.65ms) to measure the magnetic field. Magnitude images for both echos as well as the estimated field map are saved as 64×64 matrix, 192×192mm FOV, 36 3mm thick slices with 20% slice gap (effectively 3×3x3.6mm between voxel centers). When you acquire this image, remember that it must have identical spatial positioning to the fMRI scan. Acquire the first scan (fieldmap or fMRI) as normal. Then plan the second scan by dragging the sequence to the queue and right-clicking on the previous scan so you can choose the ‘Copy’ option to choose to save the slice positioning information. This will ensure that the fMRI and field map show the same regions.
- Time per volume: 6:17
- Notes: Good structural scan with excellent contrast of gray and white matter. Excellent for segmentation with VBM and coregistration with SPM and FSL.
- Protocol: This MP-RAGE sequence uses the 12-channel head-coil to acquire an image with a TI of 900ms, a TR of 2250ms between TFE shots and a 9-degree flip angle, with a very short TE (4.52ms). A total of 160 1mm sagittal slices are acquired, each with a 256×256matrix and 256×256mm FOV.
- Examples: Homogeneity corrected and spatially normalized image shown on the left. Raw scan shown on the right.
- Time per volume: 8:34
- Notes: Good scan for identifying brain injury. Typically T2 scans have very thick slices. This protocol offers a isotropic 1mm image that is great for lesion mapping and normalization.
- Protocol: This TSE scan uses a TR of 3200ms, a TE of 354ms, 256×256 matrix scan with 160 slices has 1×1x1mm resolution.
- Time per volume: 6:04
- Notes: Good scan for identifying aneurysms and stenosis. This scan highlights arterial blood. While many angiograms require contrast agents (such as Gadolinium), this sequence requires no injections (the rapidly flowing blood acts as a contrast agent).
- Protocol: This sequence uses a TR of 22ms and a TE of 3.68ms, with an 18-degree flip angle. The reconstructed image is saved as a 384×384 matrix scan with 127 slices and an interpolated 0.5×0.5×0.7mm resolution.
Diffusion Tensor Imaging
- Time per volume: 8:18
- Notes: Useful for mapping white-matter integrity. Acquisition is gated by pulse, so ensure that the participant is wearing the remote pulse sensor on a finger.
- Protocol: This 64-direction sequence uses a TR of 7300ms and a TE of 87ms, the image is saved as a 96×96 matrix scan with 60 axial slices and a 2×2x2mm resolution. The image on the right is after FSL eddy current correction, rendered using MedINRIA.