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It is not the TBSS but the dtifit, which calculates all the maps (FA, MD, etc.). You need to calculate AD and RD yourself. See Tang et al., 2012 (PNAS) for details. Briefly: ln -s L1.nii.gz AD.nii.gz fslmaths L2 -add L3 -div 2 RD Then - folllowing the tbss_non_FA guide - you need to collect all the individual maps (say AD) in a folder within your previously analysed TBSS folder. Then you can run the program. Cheers, Auer, Tibor M.D. Ph.D. MRC Cognition and Brain Sciences Unit 15 Chaucer Road Cambridge CB2 7EF United Kingdom Phone/Work: +44-(0)1223-355294 (ext. 869) Mobile: +44-(0)7906-863837<tel:%2B44-%280%297906-86-3837> Mail: [log in to unmask]<mailto:[log in to unmask]> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Rosalia Dacosta Aguayo Sent: Thursday, January 10, 2013 9:57 AM To: [log in to unmask] Subject: [FSL] Problems with AD index Dear Fsl experts, I am trying to calculate AD and RD indexes. Running tbss I got FA and MD index. As far as I know AD = L1 escalar and RD = (L2 + L3) / 2 In your TBSS/user guide, you speak about running tbss_non_FA X (X = the index I want to calculate). You speak about L2 alone, what make me a bit confused. I have created a new folder with the name AD within mytbss folder. I have copied insided all the L1 scalar resulting from running the 4 tbss steps..../home/rosi/Desktop/DTIFIT/mytbss/AD/control_aag_dtifit_L1.nii.gz but when I try to run tbss_non_FA AD it does not work, it gives me the following error: rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~$ cd /home/rosi/Desktop/DTIFIT/mytbss rosi@rosi-HP-Pavilion-dv9700-Notebook-PC:~/Desktop/DTIFIT/mytbss$ tbss_non_FA ADusing pre-chosen registration target: target upsampling alternative images into standard space control_aag_dtifit_FA ** ERROR (nifti_image_read): failed to find header file for '../AD/control_aag_dtifit_FA' ** ERROR: nifti_image_open(../AD/control_aag_dtifit_FA): bad header info ERROR: failed to open file ../AD/control_aag_dtifit_FA ERROR: Could not open image ../AD/control_aag_dtifit_FA Looking at the error message in the shell.... The question would be: is it possible I have to change the name of the files, instead of control_aag_dtifit_L1.nii.gz = control_aag_dtifit_FA_FA.nii.gz ? I suspect this could be the problem but I would like being sure about it. Yours sincerely, Rosalia Dacosta.