Here are some (very) basic/naive dwi preprocessing questions, please let me know if you have any thoughts on these.
I have two sets acquired sequentially within the same scan session (each set contains 10 Xb=0 images acquired first in the respective set, then 60 dwi b=3000; 1st set PA, 2nd set AP encode direction, 2x2x2 mm resolution)
re influence of PE direction on noise, if any: should one apply denoising to each set separately then combine outputs, or combine both sets into a dwi.mif input then run dwidenoise?
as far as I know, fsl’s topup also corrects for intervolume motion for the b=0 images selected for distortion correction.
Still, one could use both sets combined (dwi.mif) as input to dwipreproc with -rpe_all, or rpe_header flags, or use a mean b=0 (lowb.mif, 10x PA, 10XAP, resulted with dwiextract) for distortion correction, or more, use the 2-3 b=0 volumes in each set acquired closest in time to the dwi images (say lowb_3.mif, im.8,9,10 from 1st set, and 8,9,10 from 2nd set) as advised at some point. Any preferences, and if so, what would be a simple quality check (including eyeballing the dwipreproc output)?
a. several posts on this forum have addressed this, and many experts here advocate registration of T1/aparc+aseg to the dwi, so that dwi remains ‘native’, while T1/aparc+aseg could be maintained in original resolution (see Kerstin’s commands here, Registration of structural and diffusion weighted data), with transform to dwi space, usually resulting from 6 dof stored in the mif header. Could one use the same argument and transform dwi (after topup/eddy/dwipreproc) to T1 space, while keeping images at their original resolution, any issue with that (again, registration would here follow any motion/distortion correction)?
b. for cost functions, I have seen correlation ration, mutual correlation, normalized mutual info, and BBR all used for this purpose, any clear winners?
c. b=0 target image in registration, does this benefit from preparation, I have seen code examples like this (BIDS mrtrix connectome), but this is variably applied:
dwiextract dwi.mif -bzero - | mrmath - mean - -axis 3 | mrcalc 1 - -div dwi_mask.mif -mult - | mrconvert - - -stride -1,+2,+3 | mrhistmatch - T1_BET’ + fsl_suffix + ’ dwi_pseudoT1.nii’)
re: dilation for dwifod, I have seen 1 voxel (2 mm here) dilations in papers, is this what you recommend, if so how would you select n, as in
maskfilter dwi_mask.mif dwi_mask_dilated.mif -npass n.
Thank you for your prompt assist,