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Hi, > > > Hi, > > > > Is there a way to get the residuals of eddy_correction or is > > there any way to estimate a metric of suseptibility distortions > > present in DTI? > > Eddy_correction is not a model-fitting (in the way that dtifit is), > so you don't get "residuals" - however, you can look at the temporal > variance of the uncorrected and corrected datasets, though remember > that this includes variation due to the real valid diffusion effects. > To do it on either 4D dataset: > > fslmaths <4Ddata> -Tstd dataSTD > > However the majority of the variance you see here will not be related > to susceptibility distortions. The geometric distortions would be > modelled, for example, by using the FUGUE tool and a fieldmap (see > the manual for more details). Thanks for this suggestion. Unfortunately I don't have the fieldmaps and this is why I was hoping to get a measure of noise in each set. > > More generally, I need to model the imaging noise in the > > between-subject DTI analysis and I wonder if you have any > > tools < or philosophy > that address this problem. > > Again - I'm not sure this I follow - this is another separate issue - > the majority of between-subject variation will probably be neither > due to susceptibility distortions nor within-subject acquisition > noise, but due to real subject-subject variability in tract geometry > and FA values. Sure. But susceptibility distortions affect the tractography, so I was looking for an objective way to control for that. (I have of course excluded those subjects with gross distortions.) Cheers Naj