 |
 |
Ok, Thanks! Just one more question: if RD is an operation (L2 + L3) / 2....which name can write for this index? Yours sincerely, Rosalia. 2013/1/14 Anderson M. Winkler <[log in to unmask]> > Hi Rosalia, > RD isn't produced by dtifit, so if you calculate it by hand (which is > fine), you need to make sure that these files are named exactly in the same > way the other dtifit outputs (L1, L2, L3, MD, V1, etc). Check the other > filenames you have in your TBSS directory and try to emulate the exact same > names. It should work just fine. > All the best, > Anderson > > > > 2013/1/14 Rosalia Dacosta Aguayo <[log in to unmask]> > >> 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.**** >>>>> >>>> >>>> >>> >> >