Dear FSL experts,
I have another question regarding running eddy on DTI data.
For each subject in my sample, I have 2 sequences. Could you please check if my reasoning using the commands below is correct?
- First sequence includes 1 b0 followed by 30 directions + 5 additional separate b0 nifti files, all acquired with with the same value (1000 ms) and phase encoding direction. Command:
eddy --imain=file_1b0_30dir.nii.gz --mask=mask_file_created_with_5_additional_b0s.nii.gz
--acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals
--repol --out=eddy_corrected_data
- Second sequence includes 10 b0s acquired together with 90 directions (the b0s were acquired every X directions) + 4 additional separate b0 nifti files with different phase encoding direction. Command:
eddy --imain=file_10b0_mixed_with_90dir.nii.gz --mask=mask_file_created_with_10b0s.nii.gz --acqp=acqparams.txt --index=index.txt --bvecs=bvecs --bvals=bvals --topup=output_topup_using4b0_with_different_PE.nii.gz --repol --out=eddy_corrected_data