Feed synb0 topup outputs to dwipreproc

[rsmith]

Hi Qi,

As mentioned in another thread, this capability is implemented and publicly available and will be included in the 3.1.0 update, but is not present in the most recent release (3.0.2).

Dwifslpreproc output is the same as input

Quick follow-up: In the next minor MRtrix3 update (i.e. 3.1.0), dwifslpreproc will get the command-line option -topup_files, which should allow users to run synB0-DISCO independently and then feed its output to dwifslpreproc. This is already on the dev branch for anyone needing the functionality who doesn’t mind playing with git branches.

For some reason I can’t find the thread, but another user was trying to utilise:
dwifslpreproc ... -eddy_options " ... --topup=../field ..."
, which is kind of bypassing dwifslpreproc’s machinations and giving eddy a direct path to the topup output (assuming the topup output files are called “field_*” in the current working directory, and since eddy is run within the script scratch directory, the path to such needs to go up to the parent directory). But this is a hack and might require some experimentation and/or code modification.

Should I use output eddy_corrected.nii.gz as input to mrconvert to mif, denoise, and then dwipreproc?

• dwidenoise is not applicable to any image data that have undergone an image interpolation process; this includes the various corrections applied by eddy.

• Given that the principal purpose of dwifslpreproc is to execute eddy, it’s unclear why you would want to execute it on data where eddy has already been applied.

Cheers
Rob