Diffusion MRI acquisition

Introduction

Currently, there is no consensus on the "optimal" b-table setting to acquire diffusion MRI for "beyond-DTI" analysis. 10 years ago, the trend in the field 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. 

Why I am not using multi-shell acquisition?


The HCP protocol can also provide outstanding data, and many of my studies have used HCP multi-shell data to get robust results. The reason I do not use HCP scheme for my own study is that (1) the scheme is not "efficient" enough, (2) it is not invariant against rotation, and (3) intra-shell sampling is always much greater than inter-shell sampling. To be specific...

(1) the low b-value shell at b=1000 is obviously over-sampled. You can readily interpolate any DWI in the low b-shell from other DWIs, and this suggests that a lot of the diffusion samples are redundant. The same problem also happens at b=2000 shell, whereas the redundancy at 3000 is more acceptable (but still a bit over-sampled at certain directions). To reach a balance between SNR and data redundancy, the number of diffusion samples should increase with b-values. However, most multishell acquisition does not address this issue. 

(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 lower. Consequently, the scheme has a lot of "rotation variation". You may plot the sampling distribution to see this sampling homogeneity problem. This inhomogeneity may reduce reproducibility problems if the subject head is positioned at different angles.

(3) Most multi-shell acquires only 3 b-values, but could be a wide range of restricted diffusion. Using only 3 b-value may not be sensitive to a specific type of restricted diffusion. While there are ~100 samples with in each shell. It would be ideal to distribute some to capture different b-values.

Why I use a higher b-value?


My experiences applying different b-values acquisitions to neurological disorders is that at high b-values, the change of GQI anisotropy is very specific to early reversible axonal injury (e.g. early demyelination). Its specificity drops substantially for lower b-values (see last figure at Yeh et. al. Neuroimage. 2019 Nov 15;202:116131.) and will become more susceptible to physiological fluctuations, cytotoxia edema, inflammation. 

My recommendation: 11-minute q-space acquisition with b-max=4,000


My personal recommendation is an 11-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 (1)(2)(3).

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 11 minutes.  

The grid sampling has several benefits:
  1. It has uniformly distributed density in the diffusion encoding space (i.e. q-space). This avoids over-sampling at low b-values or under-sampling at high b-values. It does not have the sampling homogeneity problem in the shell acquisitions.
  2. It can be reconstructed by DTI, ball-and-sticks model, NODDI, GQI...etc.
  3. It captures a continuous range of diffusion patterns from none-restricted diffusion to restricted diffusion. For clinical studies, the grid scheme can capture all possible diffusion changes due to edematous tissue or cell infiltration. in comparison, multi-shell only acquires 2 or 3 b-values and may miss diffusion patterns that are only sensitive to values in between.
There are limitations with the grid sampling scheme:
  1. It's Eddy current artifact cannot be corrected using FSL eddy, and the bipolar pulse is often needed to handle eddy current at the sequence level
  2. Methods using spherical harmonics cannot use grid schemes because there is no shell structure for estimating spherical harmonics.
Another b0 with an opposite phase encoding direction will also be acquired to correct for the phase distortion artifact.

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.

Steps to install the 11-min q-space scheme


If you are using a Siemens Prisma scanner, you will need a C2P agreement (Talk to your Siemens representative) to install the CMRR multi-band sequence: http://www.cmrr.umn.edu/multiband/

I would recommend NOT to use Siemens' SMS because one of my user has reported serious peripheral nerve stimulation. If this has been improved, please email me and I will revise this recommendation.

The protocol PDF (QSI_258dir.pdf) and exar file at the bottom of this page. Please use the "dMRI_dir258_1" sequence. To correct for phase distortion, please add "dMRI_dir258_2", which is a copy of the former sequence with an opposite phase encoding direction. You can reduce "dMRI_dir258_2" to acquire only the b0 to save time.

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

STEP1: Download the b-table

If you are using a Siemens Scanner, you may download the vector table here: 

101 directions on grid: https://pitt.box.com/v/GRID101-BTABLE
128 directions on grid: https://pitt.box.com/v/GRID128-BTABLE
258 directions on grid: https://pitt.box.com/v/GRID258-BTABLE (recommended)

If you are using other Scanners, you may need to convert the b-table to its compatible format: https://pitt.box.com/v/GRID258

STEP2: Setup parameters


Set up the parameters for the sequence in the following steps:

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. In the diffusion tab, load the vector table obtained from STEP1 by "Free" mode.
6. b-value1=0 and b-value2=4000
7. "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 grid scheme.
8. Minimum TE and TR
9. Pixel bandwidth: ~1700
10. Phase encoding direction: A to P
11. Make a copy of the sequence, invert its phase encoding direction (P to A). Only b0 is needed here for phase distortion correction. 

STEP3: Quality Check

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 [Tool: Batch Processing][SRC 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
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)

In the analysis, copy the DICOM files from these two DTI acquisitions together.

This acquisition will require FSL's eddy to correct for the eddy correct artifact.

An important issue about motion correction


FSL's eddy is the best solution for motion correction, and I highly recommend using it if it accepts your data.

However, it is worth noting that the correction is using "data redundancy" to replace corrupted data. To be specific, motion correction routine first discards corrupted DWI volume/slices, and then the missing slices were estimated using "nearby DWI" (DWI with a similar diffusion gradient encoding). Motion correction works means that (1) several DWI samples are redundant (2) you can acquire fewer DWI samples in a shorter scanning time to get similar quality. 

An optimized sampling will have redundancy minimized, and there is no chance for motion correction. The grid sampling scheme I suggested above is close to this optimized condition. FSL's eddy will not improve its quality because there is minimal data redundancy. 

My past experience is that if there is visible motion in the acquisition, the only choice is to discard the entire scan and redo it. DSI Studio has a routine for DWI quality checks and can help identify problematic data sets.


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