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Hi Anderson, I run the four steps for calculating FA, but not for calculating the other indexes. I used FA index to calculate the other indexes with tbss_non_FA RD...for example (first I calculated RD = L2 + L3) / 2 and then tbss_non_FA RD....for other indexes different of FA some experts told me I had not to run the four steps again..... I am very confused now.... Yours sincerely, Rosalia. 2013/1/14 Anderson M. Winkler <[log in to unmask]> > Hi Rosalia, > > You need to run all the steps before trying to do non-FA analyses. Please, > see the instructions here: > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/UserGuide#Using_non-FA_Images_in_TBSS > > About GLM: randomise uses the general linear model for the regression, > just as fsl_glm, FEAT and many other applications do. What randomise does > differently is not in the regression stage, but later, when the p-values > are computed. So, when using randomise, yes, the GLM is being used behind > the scenes too. > > All the best, > > Anderson > > > 2013/1/14 Rosalia Dacosta Aguayo <[log in to unmask]> > >> Sorry Tibor, >> >> Thanks for your answer. >> >> But when I calculated the other indexes, I did not get >> all_RD_skelotonized file...because I did not run the four TBSS steps, only >> tbss_non_FA RD...for example. So, where is this file?? >> >> Yes, you are right, I mentioned randomise thinking about the Glm design >> (design.con and design.mat). >> >> Best regards, >> >> Rosalia. >> >> 2013/1/14 Tibor Auer <[log in to unmask]> >> >>> Only all_FA_skeletonised must be replaced (e.g. all_RD_skeletonised), >>> mean_FA_skeleton_mask remains.**** >>> >>> ** ** >>> >>> One remark: if I am correct, randomise is not GLM. **** >>> >>> ** ** >>> >>> 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 <%2B44-%280%297906-86-3837>**** >>> >>> Mail: [log in to unmask]**** >>> >>> ** ** >>> >>> *From:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On >>> Behalf Of *Rosalia Dacosta Aguayo >>> *Sent:* Monday, January 14, 2013 6:14 PM >>> *To:* [log in to unmask] >>> *Subject:* [FSL] One doubt running randomise with other indexes than FA* >>> *** >>> >>> ** ** >>> >>> Dear Fsl experts, >>> >>> My apologizes for this basic question. >>> >>> If I want to run randomise with other indexes than FA, it would be right >>> running the following command: >>> * >>> randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d >>> design.mat -t design.con -n 5000 --T2 -V * >>> >>> Entering in the Glm, instead of FA, the RD or MD, AD? >>> >>> Many thanks in advance for your helping. >>> >>> Your sincerely, >>> >>> Rosalia Dacosta.**** >>> >> >> >