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Hi Lau, Actually, if you're only interested in comparing size of the structure(s), you don't need to perform vertex analysis at all - instead you can perform volumetric analysis, which is a bit more straightforward: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide#Volumetric_Analysis Vertex analysis is geared towards comparing differences in shape and pose, rather than size. If you want to compare absolute sizes, you can use the volumes that you calculate directly from the native-space segmentations. If you want to normalise by brain size, you can calculate this from your BET outputs, and normalise the structure sizes with them. Paul On Dec 5 2019, at 11:37 am, Laust vind <[log in to unmask]> wrote: > Thank you for the clarification, im looking for difference in size. What would be preferable then? > > ######################################################################## > 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