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Hi Jesper, I found an an email from back in October 2017 where you wrote the following: [Subject: Applytopup to fMRI series] >In the slightly longer term we hope to release an fMRI version of eddy. The current version is >not ideal for that, but already now you can trick eddy into doing motion correction for your fMRI >data. You need to make fake bvals and bvecs files with all zeros in the first, and specify the --> b0_only flag. I was interested in using this to combine motion correction and topup into a single resampling but I can't seem to get it working properly. It seems that eddy isn't doing any sort of motion correction when the --topup flag is passed. My 4D EPI data has 40 volumes. So I made a a bvals file with 40 lines of just 0 and a bvecs file with 40 lines of 0 0 0. I I'm running eddy this way: eddy --imain=data.nii.gz --mask=mask.nii.gz --index=index.txt --acqp=acq_params.txt --bvecs=bvecs --bvals=bvals --out=eddy_corr_b0only_opt -v --b0_only --topup=topup I was using fsl 5.0.9 and so I upgraded to 5.0.11 to see if that made any difference. I had to add the --data_is_shelled option, but the result is the same. As a simple test case, I took an image, applied a rotation of 10 degrees in the X and Y planes and then merged the original, rotated, and original images and re-ran eddy: eddy --imain=data.nii.gz --mask=mask.nii.gz --index=index.txt --acqp=acq_params.txt --bvecs=bvecs --bvals=bvals --out=eddy_corr_b0only_opt_WITH_topup -v --b0_only --topup=topup --data_is_shelled Reading images Performing volume-to-volume registration Running Register Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 0, Total mss = 242.648 Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 1, Total mss = 242.648 Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 2, Total mss = 242.648 Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 3, Total mss = 242.648 Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 4, Total mss = 242.648 Running sm.ApplyB0LocationReference Running sm.WriteParameterFile Running sm.WriteRegisteredImages Running sm.RecycleOutliers Running sm.WriteRotatedBVecs Running sm.WriteMovementRMS The resulting movement parameters are just all 0s, as would be expected at this point since the mss is staying constant. If I run the exact the same command but drop the topup flag, then things appear to work, although the volumes in the eddy output are not well-aligned eddy --imain=data.nii.gz --mask=mask.nii.gz --index=index.txt --acqp=acq_params.txt --bvecs=bvecs --bvals=bvals --out=eddy_corr_b0only_opt_WITHOUT_topup -v --b0_only --data_is_shelled Reading images Performing volume-to-volume registration Running Register Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 0, Total mss = 194.67 Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 1, Total mss = 185.835 Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 2, Total mss = 170.245 Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 3, Total mss = 157.97 Loading prediction maker Evaluating prediction maker model Calculating parameter updates Iter: 4, Total mss = 146.556 Running sm.ApplyB0LocationReference Running sm.WriteParameterFile Running sm.WriteRegisteredImages Running sm.RecycleOutliers Running sm.WriteRotatedBVecs Running sm.WriteMovementRMS Have I misunderstood something or do you have any insight into what might be happening here? I realize that this wasn't the intended use of eddy but figured I'd ask since you had brought it up on the list! Thanks for any insight and for the great tools! -- Niels Bergsland Integration Director / Research Assistant Professor of Neurology Buffalo Neuroimaging Analysis Center / University at Buffalo 100 High St. Buffalo NY 14203 [log in to unmask] ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1