Hi Ludovica Thank you for the papers. Can I confirm the steps pls? 1) Create mean FA skeleton from all subjects and both time points. 3) Substract FA maps between both time points, using the mean FA skeleton in (1) as a mask. 4) Use the masked, subtracted maps for randomise analyses Does this look alright? Thanks for your help. On Thursday, May 9, 2019, 11:07:25 AM GMT+1, Ludovica Griffanti <[log in to unmask]> wrote: Hi Shane,if you are specifically interested in longitudinal TBSS analysis, there is no specific pipeline on the user guide, but here are some papers that used TBSS in longitudinal analyses that you can check:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228140/https://pubs.rsna.org/doi/full/10.1148/radiol.2015150103https://academic.oup.com/brain/article/132/9/2437/355773 Hope it helps,Ludovica — Ludovica Griffanti, PhD Postdoctoral Researcher Wellcome Centre for Integrative Neuroimaging (WIN) Oxford Centre for Functional MRI of the Brain (FMRIB) Nuffield Department of Clinical Neurosciences, University of Oxford John Radcliffe Hospital Oxford, OX3 9DU, UK email: [log in to unmask] On 9 May 2019, at 10:47 am, Matthew Webster <[log in to unmask]> wrote: Hi Shane,The TBSS User guide: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/UserGuide is probably a good starting point for this kind of analysis. Kind RegardsMatthew -------------------------------- Dr Matthew Webster FMRIB Centre John Radcliffe Hospital University of Oxford On 9 May 2019, at 10:16, Shane Schofield <[log in to unmask]> wrote: Hi FSL DTI Users,Is there any pipeline recommended by FSL for TBSS analyses (FA maps)? Appreciate any suggestions.Thanks, Shane To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1