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Hi Rosalia, this has been previously discussed on the list. Please have a look at the FSL archives with fsl-vbm lesion as keywords... One straightforward yet time-consuming approach is to mask out individually all the lesions. Once this is done, you can use the rest of the VBM pipeline as usual. Cheers, Gwenaelle -------------------------------------------------------------------- Gwenaëlle Douaud, PhD FMRIB Centre, University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717 www.fmrib.ox.ac.uk/~douaud -------------------------------------------------------------------- ________________________________ De : Rosalia Dacosta <[log in to unmask]> À : [log in to unmask] Envoyé le : Mercredi 26 Octobre 2011 23h17 Objet : [FSL] Having some problems with VBM tool Dear FSL experts, I have one question with the use of VBM tool. My patients have lesions, so I suppose that I can't use a conventional analysis with VBM. Could anyone give me some advice in relation to this situation and about these questions: 1. How calculate GM template with lesioned brains? 2. How many DOF it would better use for this kind of analysis? 3. How I could calculate the proper smoothing for my data? 4. How I could calculate sigma value? Thank you very much in advance, Best regards, Rosalia.