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1. Post screenshots; I don't know what you mean. 2. FA is never negative. I don't think MD can be, either. 3. The bvecs file is the only one containing the directions (I think). bvals contains the b-values, and the nii file is the image itself. 4. Read papers by Behrens et al. and Jbabdi et al. to learn what bedpost does. 5. I could be wrong, but step 2 might just compute the registration, whereas step 3 actually applies them to the data. On 09/23/2014 01:52 PM, Francesco Puccettone wrote: > > Hi everybody, > > > There are some things which I don't understand from my DTI analyses: > > > 1. Why does my all_FA_skeletonised image have a gray line outlining > the brain's outer contour, when clearly the edge of the brain does not > contain white matter, let alone skeletonised white matter? Are these > values ignored in the analyses, or are they artefacts in how > all_FA_skeletonised was created? If so, what causes this artefact, and > how to get rid of it? > > > 2. I know that FA values close to zero reflect isotropy of water > diffusion, i.e. non-coherent fibre bundles, whereas the opposite > (anisotropy) is true for FA values close to 1. However, I know that > the range of FA values is from -1 to 1. What do negative values of FA > mean, and does it make sense to ignore the sign and just think of the > *absolute value* of the FA index as a measure of white matter > integrity? Also, how does this observation hold for non-FA measures > such as MD? > > > 3. Why aren't all diffusion directions contained in a single BVAL, > BVEC and NII file, instead being split into 3 files of each type (with > 21+22+25 diffusion directions)? > > > 4. If the diffusion model per se is generated by DTIfit, and the > specific bundles are later tracted by ProbTrackX, then what exactly > does the BedPostX step of the pipeline do that is not either of these > previous operations? > > > 5. What is the difference between step 2 of TBSS, which "runs the > nonlinear registration, aligning all FA images to a 1x1x1mm standard > space", and step 3, which "applies the nonlinear transforms found in > the previous stage to all subjects to bring them into standard space"? > > > Thank you very much for your kind help! > > --Francesco >