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Dear Baixiong, you might also want to consider using eddy instead of eddy_correct. It is a new(er) tool that performs considerably better than eddy_correct. Jesper Hi Baixiong, Assuming that you properly ran DTIFIT between eddy_correct and your calculation of RD (L23) to get your diffusion maps, then I'd agree that all makes sense. (I'm less familiar with fslroi to extract volumes from a 4D dataset though; you might find fslselectvols to be more intuitive if you're only wanting to grab one volume from a 4D dataset). Iain On Wed, 19 Jun 2019, 12:30 Baixiong Xiao, <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear all, I installed version fsl6.0. I preprocessed DTI data using the following scripts: is that right? is that enough? fslroi MS01.nii.gz b0 0 -1 0 -1 0 -1 0 1 Bet2 b0.nii.gz nodif_brain –m –f 0.3 eddy_correct MS01.nii.gz data 0 Get L23: fslmaths L2_image -add L3_image -div 2 L23 Best Baixiong ######################################################################## 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