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Hi - perhaps you can use FIRST on the individual structurals (if you have T1-weighted data) then transform these to diffusion space? Alternatives are: - use a weighting mask in FLIRT to make registration better around the caudate/ventricle area - use FNIRT on FA images and the FMRIB58 atlas as a target Saad On 29 Nov 2011, at 03:56, Yadi wrote: > Dear FSL experts, > I want to make masks of subcortical grey matter structures in DTI native space,so that i can get mean FA/MD value of each structure.I used flirt to get diff2standard.mat.Diff2standard.mat was converted to standard2diff.mat which was applied to each mask in standard space(MNI152).Finally,I used fslmaths to adjust these masks.Most of these masks ,such as thalumus and caudate,matched the structures.However,caudate masks in many subjects got poor match to the same-name structures and cover part of anterior limb of internal capsule.Can anyone help me out?Thanks! > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad