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For an estimate of noise wouldn't that be as simple as measuring the SNR of the diffusion weighted images? Susceptibility distortions often cause issues when trying to register a DTI dataset to a structural one. Perhaps you could evaluate the quality of your registration of the FA to the T1 structural image, should you have acquired one? Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Tim Behrens Sent: Tuesday, October 16, 2007 9:03 AM To: [log in to unmask] Subject: Re: [FSL] DTI: noise estimation The only thing I can think of it to use the variance map from bedpostx e.g. flsmaths merged_phsamples -Tstd std_ph flsmaths merged_thsamples -Tstd std_th fslmaths std_ph -add std_th std_both fslstats std_both -M you could even use a mask of the susceptibility region, but I don't know who accurate a measure this will be, particularly given that you will only have 50 samples at each voxel. Might be worth a try tho' T On 16 Oct 2007, at 13:40, Najmeh Khalili M. wrote: > 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