Dear MRTrix Community,
I acquired a DWI dataset using the following parameters:
- multi-shell including b=400, b=1000 and b=2000 s/mm2 with 32, 32 and 60 directions for each shell + 8b0s (Total of 132 volumes);
- voxel size: 2 mm3;
- TR/TE=6800/89 ms;
- acceleration factors: SMS=3; GRAPPA=2.
As so, I have a few questions regarding the optimal parameters set for dwidenoising and mrdegibbs preprocessing steps.
- I applied dwidenoising to the images extracted directly from the scanner. Then, I tested 2 extent sizes besides of the default size. However, I got confusing results in comparison to the recommendations. See attached pdf file (noise map+rms of residuals). What are your thoughts about these results? It seems to me that the most appropriate extent to be applied is ext3. Since I am using multiband, my data has spatially varying noise, right? So, I should be using a kernel size N~M -> 5x5x5 = 125 ~132 volumes, right? However, the results seem to contradict this recommendation:
For maximal SNR gain we suggest to choose N>M for which M is typically the number of DW images in the data (single or multi-shell), where N is the number of kernel elements. However, in case of spatially varying noise, it might be beneficial to select smaller sliding kernels, e.g. N~M, to balance between precision, accuracy, and resolution of the noise map.
For mrdegibbs correction, how can I decide what is the most appropriate set of parameters (nshifts, minW, maxW)?
For both corrections, do you have any quality control metric that can be used to evaluate the quality of the corrections performed or only visual inspection is advised?