Diffusion MRI acquisition

Current Trend in Diffusion 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 is over-sampled because any of its DWI signals can be readily interpolated by other similar DWIs. In comparison, the high b-value samples does 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 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 an 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 (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 12 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 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 are strategies I recommend to optimize the DWI protocol

(1) Reduce scanning time using multiband (MD=3 or 4)
(2) shorten TE by partial Fourier PE 
(3) shorten TE by high readout bandwidth (trade-off with SNR)
(4) Phase distortion correction by acquiring full-forward PE and one b0 at backward PE

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 12-min q-space scheme on Siemens scanners

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/. 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).

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.

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" and acquire only the b0 (take only few seconds). "dMRI_dir258_2" is a copy of the former sequence with an opposite phase encoding direction.

The 12-min grid-258 vector table can be found here: 

grid-258: https://pitt.box.com/v/GRID258-BTABLE (recommended)

If you would like to further reduce the scanning time, the following b-table can be useful:

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 b-table to its compatible format: https://pitt.box.com/v/GRID258

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. 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. 

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 [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.

Preprocessing Protocol

1. Rename DICOMs: 

Click on [Batch Processing][Step B1: Rename DICOM n Subfolders] and specify the folder that contains the DICOM files. DSI Studio will rename the DICOM files and create new folders storing them. This step can be done for multiple subjects in one shot. You may remove the original folders after it is done.

2. Create SRC and NIFTI files: 

Click on [Batch Processing][Step B2: Create SRC/NIFTI files] and specify the folder that contained the renamed DICOM files. DSI Studio will create SRC files and place them under the "src" folder, one for each scan session. The T1W images or other structure images will be created and placed under the "t1wt2w" folder. Please note that the PA b0 file (e.g., xxxxx_dMRI_dir258_PA_SBRef.nii.gz) will also be created and placed under the same folder.

3. Move SRC files together:

Each SRC file store the all DWI for each scan session. I would suggest copy all SRC files to one folder to proceed with the analysis. You may also rename the SRC files to remove date information.

The following analysis can follow the other documentations: Batch processing using GUIDiffusion MRI Reconstruction in DSI StudioCreate a connectometry database

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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