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Hi Anastasia, > Gwenaelle, > > When you say that I can draw my ROI on MNI_T1 1mm template, > do you mean the > actual MNI template or my structural scan registered to > MNI_1mm using FNIRT? I mean the MNI template (or the FMRIB58 template). Drawing one set of ROIs in the standard space is easier, faster and presumably more consistent across subjects. Then you need to inverse the warpfield generated by TBSS from your native FA to the FMRIB58 to place tis set of ROIs in the *native* diffusion space of each subject for the tractography (again, probtrackx in the standard space is not accepting NL registration parameters yet)... Cheers, Gwenaëlle