I would like to discuss several aspect of preprocessing of my dwi data and dwipreproc script internals:
Some of my DWI data are acquired only at one phase encoding direction. However, I also have 2 additional series of epi B=0 only data acquired at both AP and PA directions. These are with different voxel sizes that main DWI series.
I was thinking to achieve distortion correction by resampling the additional B=0 series to resolution of main DWI and use them with -rpe_pair option. I was looking to the dwipreproc code how this functionality is implemented and it seems that there is no registration of -rpe_pair series to main DWI done to correct for possible subject movement.
The user guide of eddy says in context of --field option (but I think that this also applies for this case):
“If the first volume input to topup is the same as the first volume in --imain to eddy, the fieldmap will automatically be in the reference space of eddy. When using the --field option the user is responsible for making sure the fieldmap is registered to the eddy data.”
So it seems to me that if the -rpe_pair option is used, the first volume of the first file of -rpe_pair has to be identical to the first volume of main DWI, otherwise it would not work correctly in case of subject movement.
Could you please comment on?
I also tried to do the processing by hand by fullfilling the “identical volume” condition I mentioned in previous paragraph. But this time I am not sure how to correctly use dwidenoise tool in combination with eddy. I can use dwidenoise only for main DWI data, since additional AP-PA B=0 series has to be resampled first (due to different voxel size wrt main dwi) and dwidenoise cannot be used before resampling due to low number of volumes (three for each direction). Therefore, I concatenated resampled B=0 AP and PA series (without dwidenoise) with main DWI (with dwidenoise) to one volume and processed by eddy, together with output of topup done on B=0 AP and PA series. However, I am not sure if it is not the problem for eddy to process data with varying noise level. What do you think?
In other my data, I also have DWI only at one phase encoding direction. But, this time, I have gradient echo-based fieldmap. Do you plan to incorporate also this type of distortion correction to dwipreproc script?
In https://github.com/BIDS-Apps/MRtrix3_connectome repository I noticed the -rpe_header and -topup_images options of dwipreproc script. However, I did not find any of these parameters in current dwipreproc code in mrtrix3 repository. Where they came from and what is their significance?