IntroductionCurrently there is no consensus on the "optimal" btable 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. Nonetheless, the multishell acquisition has optimization problems. For example, the human connectome project acquired 90-90-90 directions at b-values of 1000, 2000, and 3000. These 90 sampling directions are not homogeneously distributed on each shell. Some directions have higher sampling density, whereas others have lower. Moreover, the 90 directions at lower b-value could be over-sampling, whereas the 90 directions at high b-value could be under-sampling. This is evident if we calculate the correlation between any two DWI in each shell, the correlation is much higher in the low b shell, suggesting greater data redundancy. My personal recommendation is "grid-258" sampling, 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. Using a multi-band sequence with an MB factor of 3, the 2-mm dMRI acquisition can be done in 15 to 20 minutes.
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 scanners, and a similar protocol may be implemented in other manufacturers. STEP1: Download the b-tableIf you are using a Siemens Scanner, you may download the vector table here: https://pitt.box.com/v/GRID258SIEMENSIf you are using other Scanners, you may need to convert the b-table to its compatible format: https://pitt.box.com/v/GRID258 STEP2: Install a multi-band EPI sequenceThe MRI scanner needs to have a multi-band diffusion sequence installed. For example, the CMRR multi-band sequence: http://www.cmrr.umn.edu/multiband/ or you may use any multi-band sequence provided by the MRI vendor. There could be a licensing fee with the multi-band sequence. *Make sure that the sequence allows for loading an external b-table (e.g. the "Free" mode) STEP3: Setup parametersSet 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. 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. *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. The good news is that you can use 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 setting 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 correctionFSL'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 less DWI samples in a shorter scanning time to get a 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 check and can help identify problematic data sets. |
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Diffusion MRI acqusition
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Siemens vector table