Hi Mark, Thanks for the clarification. But my question is why those two options are used in eddy_correction. --- Are those options used to improve the estimation of the diffusion tensor parameters? --- I find that some people use the default flirt command without using any options to preprocess the DTI scans so I tried that way and found that the estimated FA maps are different from the one using eddy_correct. So I wonder which method should I use. Best, Leo On Tue, Apr 3, 2012 at 6:50 AM, Mark Jenkinson <[log in to unmask]> wrote: > Dear Leo, > > The -nosearch is to stop an *extensive* initial search of rotation angles. > It does not the optimisation method from finding non-zero rotations, and > you will find that it does in fact correct for rotations. > > The -paddingsize is to make sure that end slices are not lost due to small, > half-voxel shifts of the FOV. This just copies the intensities from the > nearest end slice into any areas which have fallen outside the original FOV > by up to 1 voxel. > > All the best, > Mark > > > > > On 2 Apr 2012, at 23:27, Yiou Li wrote: > > > Dear FSL experts, > > > > Could you please advise the reason of using the -nosearch and > -paddingsize 1 in the flirt command in eddy_correct? > > > > It seems to me that -nosearch constrains (or turn off?) the rotation in > registration transformation -- is this because rotation transfomation could > introduce artifacts in estimation of diffusion parameters? > > > > Thanks in advance! > > Leo > > > > >