Hi all,
We’ve acquired multishell data (b = 0, 300, 700, 2000) using a 3T scanner with a multiband factor of 3. We’ve also acquired a pair of b0s (one in AP the other in PA). After running TOPUP and EDDY, I noticed some parts of the brainstem are more distorted in post-topup/eddy compared to before. Of note, I’m preprocessing my data using MRtrix’s dwifslpreproc command which relies heavily on FSL’s TOPUP and EDDY. Here are the commands:
topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/FSL/6.0.7.3-conda/etc/flirtsch/b02b0.cnf --verbose
Data is padded as it had non-even size in one of the axes
applytopup --imain=dwi_pad2_pe_0.nii --datain=applytopup_config.txt --inindex=1 --topup=field --out=dwi_pad2_pe_0_applytopup.nii --method=jac
eddy_cuda10.2 --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --topup=field --slm=linear --mporder=6 --data_is_shelled --cnr_maps --repol --slspec=slspec.txt --out=dwi_post_eddy --verbose
Raw data:
Preprocessed:
All other distortions such as in temporal or frontal are corrected. Any comments are appreciated.
Best,
Amir