Hi everyone,
I’ve seen a few threads about using Synb0 output in dwifslpreproc but they were from a while ago and the solutions mentioned there are not working for me. If anyone knows how synb0 results are supposed to be passed to dwifslpreproc I’d appreciate any pointers!
I tried what is described here Synb0 for dwifslpreproc: How?, i.e. for_each sub* : dwifslpreproc IN/dwi/PRE_denoised_dwi.mif IN/dwi/PRE_denoised_preprocessed_dwi.mif -fslgrad ../../sourcedata/IN/dwi/*bvec ../../sourcedata/IN/dwi/*bval -rpe_none -pe_dir AP -readout_time 0.0365754 -eddy_options " /home/rds/hpc-work/synb0/OUTPUTS/topup" , which returned the error message /home/rds/hpc-work/synb0/OUTPUTS/topup: is an unrecognised token!.
Also I think there has been a small change in the synb0 code since that discussion because it does not create OUTPUTS/topup when I run it, so for the purpose of this I created the OUTPUTS/topup directory and moved the 4 topup outputs (topup_movpar.txt, b0_all_topup.nii.gz, b0_all.topup_log, topup_fieldcoef.nii.gz) into it. I’m not sure if this is where the issue lies.