Hi all,
I’m having a problem while running the dwifslpreproc command on DWI volumes acquired on phantom data. The data consist of 3 runs of the same acquisition protocol (33 volumes each, with 6 b0s acquired in AP direction), with an additional reverse PE b0 acquired in PA direction.
Checking intermediate files, the field map from topup seems ok for my acquisition protocol and the volumes going inside of eddy seems correct as well. The problem arise at the end of the correction, where a shift in the PE direction appears on the b4000 shell that was not there in the raw or topup images.
Here’s the command I used:
dwifslpreproc "${denoise_mif}" "${preproc_mif}" \
-rpe_pair \
-pe_dir "${PE_DIR}"\ #AP
-se_epi "${se_epi_pair_mif}" \ #Mean b0s in AP, concat with b0 PA
-align_seepi \
-eddy_option "${eddy_opts}" \ # "--data_is_shelled --flm=quadratic -slm=linear --repol"
-eddy_mask "${mask}"\ #mask from dipy
-nthreads "${NTHREADS}" #24
Thank you all for your help,
Philippe