Hi, I just wanted to follow up on this as some subjects still seem to be getting processed without TOPUP, although the program recognizes the presence of the fieldmaps during BIDS validation. Do you have any suggestions on how to amend this? The alternate workflow these subjects seem to be getting processed with is as follows:
"Any images with a b-value less than 100 s/mm^2 were treated as a b=0 image. MP-PCA denoising as implemented in MRtrix3’s
dwidenoise[@dwidenoise1] was applied with a 5-voxel window. After MP-PCA, Gibbs unringing was performed using MRtrix3’s
mrdegibbs [@mrdegibbs]. Following unringing, B1 field inhomogeneity was corrected using
dwibiascorrect from MRtrix3 with the N4 algorithm [@n4]. After B1 bias correction, the mean intensity of the DWI series was adjusted so all the mean intensity of the b=0 images matched across eachseparate DWI scanning sequence.
FSL (version 6.0.3:b862cdd5)'s eddy was used for head motion correction and Eddy current correction [@anderssoneddy]. Eddy was configured with a q-space smoothing factor of 10, a total of 5 iterations, and 1000 voxels used to estimate hyperparameters. A linear first level model and a linear second level model were used to characterize Eddy current-related spatial distortion. q-space coordinates were forcefully assigned to shells. Field offset was attempted to be separated from subject movement. Shells were aligned post-eddy. Eddy’s outlier replacement was run [@eddyrepol]. Data were grouped by slice, only including values from slices determined to contain at least 250 intracerebral voxels. Groups deviating by more than 4 standard deviations from the prediction had their data replaced with imputed values. Final interpolation was performed using the
Several confounding time-series were calculated based on the
preprocessed DWI: framewise displacement (FD) using the
implementation in Nipype [following the definitions by @power_fd_dvars].
The head-motion estimates calculated in the correction step were also
placed within the corresponding confounds file. Slicewise cross correlation
was also calculated.
The DWI time-series were resampled to ACPC,
generating a preprocessed DWI run in ACPC space with 1mm isotropic voxels."
Thank you so much for your help!