We have run the distortion correction of dwi data based on T1w on the test dataset (as provided with Brain Suite) and also on one subject (dwi + T1w) collected at our institution. In both cases, when overlaying the dwi.nii.gz file with the dwi.RAS.correct.nii.gz, we have observed that the distortion correction applied is minimal. Is there anything we could possibly not doing correctly? For the test dataset we are simply running:
I’m starting with BS too because of the possibility of correcting EPI distortions with T1-weighted images.
I used both the –dwi-mask and –t1-mask in order to improve the correction following your advice, but the outcome was pretty the same. In fact, the outcome was even worse when I used one (–dwi-mask) or both masks (dwi+t1) than when I did not use any of them.
Maybe without a fieldmap and only a T1 little correction could be made? Don’t get me wrong, I’m quite glad with correcting at least a little of such distortions than leave my DWI volumes with such disturbances.