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Dear FSL experts, We have acquired three SE images in the AP direction and three SE images in the PA direction, and we want to use them to correct susceptibility-induced distortion in BOLD data using topup. The phase encoding direction of the functional data is PA. SE and BOLD images were acquired using the same geometry (resolution, FOV, matrix size) and matching bandwidth and echo spacing. We used the following commands: topup --imain=SEAP_SEPA.nii.gz --datain=acq_param.txt --out=topup_ --iout=topup_iout --fout=topup_fout --config=b02b0.cnf applytopup -i TASK.nii.gz -a acq_param.txt -x 4 -t topup_ -o task_topup -m jac SEAP_SEPA.nii.gz contains three SE AP images followed by three SE PA images. It was created merging in time with fslmerge. acq_param.txt is: 0 -1 0 0.1 0 -1 0 0.1 0 -1 0 0.1 0 1 0 0.1 0 1 0 0.1 0 1 0 0.1 We have observed that SE images seem to be tilted even though they were acquired consecutively. SE AP: https://drive.google.com/open?id=1MJcR_DykPXUf1EbElF5ZucT-IRquAn1T SE PA: https://drive.google.com/open?id=1UW6OaVV8zEfOX10vbiWLCJAnf-EzfSxu We notice that this tilt could be affecting the results of the distortion correction process. Corrected BOLD: https://drive.google.com/open?id=1gwsKa_0QEidADLLMcFCPnRGBkXWfjlEK I am attaching the original spin echo images, the corrected SE image (topup_iout image) and the BOLD image corrected by using applytopup. Do you think the imperfect correction is due to something wrong with the processing steps or something strange going on with the original SE images? SE AP: https://drive.google.com/open?id=1y8cbUAk1pI3O0CK22PNWAUftMJKfel5Y SE PA: https://drive.google.com/open?id=1xzqY1_mTfCbORt75ruVdCqVKsMbKg-q9 Topup_iout: https://drive.google.com/open?id=1zXyOFIbDPLiRCKO4FoKPw5weW9GxCJF9 Corrected BOLD: https://drive.google.com/open?id=1QEE7ZqV2a2qowQyzQxGEJ6tSCPktUs4F We have also acquired field maps in the same session to compare distortion correction results. FEAT: https://drive.google.com/open?id=17VR5MAmNrsgZJfsfcYNr8nD6S2SmY1GS Would it be better to correct distortions using topup or using fieldmap via FEAT?