Hi FSL users/experts,
I'm working on a diffusion MRI dataset (n = 92) with multiple b-values (700, 1000, 2000). I've preprocessed the data using MRtrix's dwifslpreproc but my question is FSL-related. I applied EDDY and TOPUP from FSL v6.0.7.3 to that preprocessing pipeline with the following flags for eddy: --slm=linear --mporder=# --data_is_shelled --cnr_maps --repol. Of note, I used the -rpe_headers flag for MRtrix so it can obtain all the PE dir and TotalReadout automatically from the headers.
After completing preprocessing and running SQUAD I got an error on "topup acquisition parameters" (data_eddy_para from the accompanying qc.json). I listed these values for my subjects and it seems that there are 7 types of data_eddy_para (n in each = 59, 18, 11, 1, 1, 1, 1; total 92) in which the TotalReadout and in some instances, the PE-dirs are different. The differences in the total readout are in the order of 1e-06 for some cases. How can I reliably do a study-wise quality control?
Best,
Amir
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