Current Trend in Diffusion MRI Acquisitions

There is still no consensus on the “optimal” b-table setting to acquire diffusion MRI for “beyond-DTI” analysis. 10 years ago, the mainstream beyond-DTI acquisition was “high angular resolution diffusion imaging” (HARDI), which acquires hundreds of sampling at one b-value (typically 3000 or more), but then HARDI was gradually replaced by multishell acquisition, which acquired diffusion MRI using at least two different b-values. This trend was motivated by studies confirming the benefit of combining data from multiple b-values.

Recently, the multishell acquisition has been used in the HCP protocol to get robust results, but the protocol has the following issues:

  1. The 90 sampling directions at the low b-value shell are over-sampled because any of its DWI signals can be readily interpolated by other similar DWIs. In comparison, the high b-value samples do not have a lot of redundancy. An optimal setting should have similar redundancy for each shell, and this means high b-value shells should have more sampling directions.
  2. In addition to the efficiency problem, the sampling density is largely inhomogeneous within each shell. Some directions have a higher sampling density, whereas others have a lower. Consequently, the scheme has a lot of “rotation variation”. This inhomogeneity may reduce reproducibility if the subject head is positioned at different angles.
  3. The multi-shell acquires only 3 b-values, and it would be ideal to sample at more b-values to better differentiate restricted diffusion.

My recommendation: 23 b-values with b-max=4,000 at 258 directions

My personal recommendation is a 12-minute “grid-258” sampling with a maximum b-value of 4000, which acquires, not just two or three b-values, but 23 different b-values ranging from b=0 to b=4000 at a total of 258 directions. The low b-value range has fewer sampling compared to HCP multi-shell, making the entire acquisition much more efficient. Moreover, the scheme reaches a higher b-value to 4,000 so that it captures restricted diffusion much better. This scheme addresses the above-mentioned 3 issues in multi-shell acquisitions.

Using a multi-band sequence (e.g. CMRR) with an MB factor of 4, this 2-mm 258-direction dMRI acquisition can be done in 12 minutes.

The grid sampling has several benefits:

There are limitations with the grid sampling scheme:

The following steps will help you set up the grid-258 sampling scheme on your MRI scanner. The following steps are verified on Siemens Prisma scanners, and a similar protocol can be implemented in other manufacturers. If scanning is an issue, you may also consider grid-101 (b-table here)

Steps to install the 12-min q-space scheme on Siemens scanners

The following are strategies I used to optimize the DWI protocol

If you are using a Siemens Prisma or Skyra scanner, you will need a C2P agreement (get it from your Siemens representative) to install the CMRR multi-band sequence: http://www.cmrr.umn.edu/multiband/. You may also need a Siemens SMS EPI license (for MB imaging), Siemens DTI package license (for diffusion table), High-performance gradient (HCP) that is installed in Prisma (for high bandwidth readout).

Then setup the sequence using the exar file:

Please use the “dMRI_dir258_1” sequence and add its opposite phase encoding b0 acquisition “dMRI_dir258_2” (take only few seconds).

In the diffusion tab of the sequence, switch “MDDW” to “Free” mode and load the grid-258 b-table. The grid-258 text file should be placed under C:\MedCom\MriCustomer\seq. You may need to rename the current DiffusionVectors.txt file to another name first and then copy the grid-258 table to DiffusionVectors.txt. Then set b-value1=0 and b-value2=4000

I would recommend NOT to use Siemens’ SMS-DWI for DSI-258 because my collaborator has reported serious peripheral nerve stimulation. If this has been improved, please email me and I will revise this recommendation.

If you are using other scanners, please follow the following instruction.

Steps to install the 12-min q-space scheme on Other scanners

If you are using other Scanners, you may need to convert the grid-258 b-table to its compatible format.

The following are acquisition parameters:

  1. In-plane resolution: 2.0 mm, slice thickness: 2.0 mm (if your SNR is not good enough, increase them to 2.4 mm.)
  2. Matrix size: 104x104
  3. Slice number: 72 (can be reduced if ignoring the cerebellum), no gap
  4. Multi-band acceleration factor: 3 or 4
  5. “Bipolar” diffusion scheme (for eliminating eddy current). Some may prefer “Monopolar” and correct Eddy current using FSL’s eddy. This only works on shell acquisition, and I do not recommend this approach for the grid scheme.
  6. Minimum TE and TR
  7. Pixel bandwidth: ~1700
  8. Phase encoding direction: A to P
  9. Make a copy of the sequence, invert its phase encoding direction (P to A). Only b0 is needed here for phase distortion correction.

Quality Check for Preliminary Results

  1. Make sure that you can still see the brain contour in the DWI with b=4000. If not, consider lowering the b-value to 3000.
  2. Create SRC files from the diffusion MRI data. Run DSI Studio and use [Diffusion MRI Analysis]Step T1a: Quality Control to select a folder that contains the SRC file. It will compute “Neighboring DWI correlation”. The one with a low correlation value may indicate a problem in data acquisition.

Please feel free to send me your grid258 data for a quality check. I will compare the results with the data I have to make sure that you have achieved the same quality.

What if I only have the default DTI protocol?

The good news is that you can use the scanner’s built-in DTI protocol to acquire “multishell” and still enjoy the benefit of “beyond-DTI” methods such as GQI, QSDR, RDI…etc.

Here’s a working parameter on a SIEMENS 3T Scanner:

  1. acquire one 32-direction DTI at b=1500 and another 60-direction DTI at b=3000 (built-in ep2d_mddw protocol)
  2. In-plane resolution: 2mm, slice thickness: 2mm (isotropic resolution is important) If scanning time is an issue, use 2.5 mm isotropic.
  3. Matrix size: 104x104
  4. Slice number: 72 (can be reduced if ignoring the cerebellum), no gap
  5. Minimum TE and TR, but the TE for the b=1500 DTI should be the same as the TE of the b=3000 DTI.
  6. Make a copy of the sequence and invert its phase encoding direction (acquire AP and PA for phase distortion correction)