PROBE 3D CSI

General

• Practical examination times range from 9 to 35 minutes.
• The 3D CSI reconstruction process creates 256 small chemical shift images that are stored as a standard MR image. The complex CSI storage images, two for each slice - i.e., real and imaginary - are stored in a separate series. The CSI images span the frequency range from 4.3 to 0.49 PPM. Spectra and metabolite maps for each slice along the third dimension are extracted from the individual CSI images with the READY View CSI Spectroscopy workflow.
• It is possible to acquire 3D CSI spectra from volumes smaller than 1 cc if there is sufficient SNR, as may be possible with a surface coil. For example, for Freq = Phase = 8, and FOV = 4, CSI Slice Thickness = 5, then the CSI volume = 0.125 cc = 4/8 × 4/8 × 0.5.
• PROBE-P is compatible with surface coil acquisitions.
• You may also use the body coil but low SNR will often be a problem.
• The procedure used to define the CSI voxel in Graphic Rx is critical. Follow the instructions in PROBE 3D CSI: acquire a scan so that when you select the series from which you defined the VOI location and the spectroscopy series and then click READY View, the localizer image appears in the READY View lower left viewport.
• If Auto Prescan is successful, the receive and transmit gains, the center frequency, the linewidth, the flip angle of the water suppression RF pulses, and the water suppression level are displayed, such as, "R1:11, R2:29, AX:63855957, LnWdth:10, Flip Ang:145, Supp Lvl:98.
• The LnWdth value is critical to the success of a spectroscopy scan. The shim process (part of APS) attempts to improve the homogeneity through the voxel by adjusting the gradient currents. The linewidth value is a measure of the voxel homogeneity; the smaller the linewidth, the better the homogeneity.

Scan parameter

• FOV: The FOV affects the size of the 3D CSI phase encoding volume and the size of the CSI voxels.
• Frequency/Phase: Increasing Freq and Phase (and # CSI Slices in the third dimension) increases spatial resolution and scan time. For a TR = 1000 ms, scan times increase with matrix size as (the actual times are a few seconds longer in each case):
  • 8×8×8 = 512 = 8:32
  • 16×8×8 = 1024 = 17:04
  • 10×10×x10 = 1000 = 16:40
  • 12×12×12 = 1728 = 28:48
  • 16×16×16 = 4096 = 68:16
• Phase matrix: Freq, Phase, and # CSI Slices define the 3D CSI phase encoding matrix.
  • The 3D CSI phase encoding volume = FOV × FOV × # CSI Slices × CSI Slice Thickness. The PRESS volume is equal to the area of the ROI × Voxel Thickness. The nominal volume of the CSI voxels is (FOV/Phase) × (FOV/Freq) × CSI Slice Thickness. For example, for FOV 24 cm, CSI Slice Thickness 10 mm, Freq 16, and Phase 16, the nominal CSI voxel volume is 2.25 cc (= 24/16 × 24/16 × 1).
• ROI: The PRESS ROI must be smaller than the FOV. If you prescribe an ROI that is larger than the FOV along either in-plane dimension, an error message is posted on the Scan desktop. The ROI must be resized before any other inputs or command selections are allowed. Resize the ROI until the error message is no longer displayed.
• Scan plane: For graphic prescription of the PROBE-P volume, the plane of the localizer images must be the same as the prescribed plane. For example, an axial VOI is prescribed on an axial localizer.
• Slices per Slab: It is the number of phase encoding steps in the third dimension of the 3D CSI phase encoding matrix. Allowed values are 8, 10, 12, 14, and 16.
• Slice thickness: The 3D CSI SNR depends on TE, TR, NEX, Freq, Phase, and # of CSI Slices and CSI Slice Thickness.
  • CSI Slice Thickness is the depth or third dimension of the 3D CSI voxels. Select the first item on the CSI Slice Thickness menu; this value is calculated to produce an isotropic CSI volume. Cubic or isotropic 3D CSI volumes are recommended. One cubic centimeter (1 cc) nominal CSI volumes provide reasonable SNR and spatial resolution when using the head coil. If the FOV = Freq = Phase, each edge of the CSI pixel is 1 cm in length. CSI Slice Thickness determines the length of the third dimension, and for CSI Slice Thickness = 10 mm the volume is 1 cc.
• TE: Use TEs longer than 100 ms for CSI acquisitions.
  • For TE 144 ms, the lactate doublet is inverted relative to the long T2 species such as the creatine, choline, and N-acetyl resonances.
  • The lactate doublet is fully refocused at TE 288 ms, but even the signals from the long T2 species experience substantial decay, and therefore the 288 ms choice is not recommended.
• TR: A TR of 1500 or 2000 ms enables the comparison with spectra acquired with PROBE-P in its single voxel mode.
  • Use the same TR so that you can compare spectra acquired on different dates, or in different patients.
• Voxel thickness: It must be smaller than # of CSI Slices × CSI Slice Thickness.
  • While the Voxel Thickness can range from 3 to 100 mm, values between 30 and 45 mm are typical – low homogeneity over large volumes is the limiting factor.

User CVs

Click the Advance tab to view the available User CVs. The CVs may vary based on the field strength and selected scan and imaging parameters.

• Automatic Water Suppression Optimization
• ROI Edge Mask SAT
• Scan mode
  • 3D CSI reconstructions also depend on the number and spacing of the reference images within the prescribed PRESS volume, and on your scan mode selection. If you set the Scan Mode User CV to 2, the CSI images are reconstructed as prescribed. The number of CSI slices is equal to your # CSI Slice selection. If # of CSI Slices = 8, then 8 CSI images are reconstructed. However, if Scan Mode = 1, Fourier interpolation and the Fourier shift theorem are used to reconstruct the CSI images centered on the centers of the reference images that fall within the prescribed PRESS volume.

Post-process tasks

There are multiple compatible post-process tasks. For details, see Add post-process task.

• Brain Spectroscopy (2D & 3D CSI)
• Image Enhancement Filters