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We used two types of masking. First, the white matter skeleton produced by tract-based spatial statistics (TBSS, Smith et al, 2006) was used as a mask. This skeleton defines the central find more points of large white matter tracts, and thus provides a robust method of focusing the voxel-wise analysis on locations where the risk of partial volume effects is low. We generated the skeleton considering the 10 subjects from which the template was generated, then we considered the other 11 healthy subjects, and finally all 21 healthy controls. As can be seen in Supplementary Fig. 1, very similar results were obtained considering the different groups. Second, a CSF mask produced by FAST (Zhang et al, 2001) and the grey matter masks of start and target regions were used to further limit the extent of the tract template. DTI measures from the individual tractography and tract template approaches were then compared in three configurations: 1) no masking; 2) white matter ��skeleton�� masking; and 3) ��skeleton��?+?CSF?+?ROIs masking. Spearman's correlation statistics were used for mean MD and FA values. We performed the same set of analyses on a further group of 11 control subjects, who had not been used to generate the template tracts. This was done to test whether the tract templates could be applied outside the original group. We then U0126 in vitro directly tested whether individual tractography in the patient group was problematic. Tractography was performed using the same procedure as for controls. We calculated diffusion measures for the resulting tracts, and we also determined estimates of dispersion of the principal and second diffusion direction at each voxel. This provides a measure of the noise, and hence the uncertainty, of the estimation of the diffusion direction when sampling from its probability density function. We hypothesized that dispersion would be increased in patients as a result of the white matter damage caused by TBI. FA and MD maps of patients were non-linearly registered to MNI space using FNIRT (Andersson et al, 2008). FA and MD values were then sampled using the tract templates defined in the control group. Building on the results of the experiment LMTK2 described in above, both masking techniques (TBSS skeleton and CSF masking) were used in the patient analyses. We predicted that increasing white matter damage would result in a greater discrepancy between the two approaches, because individual tractography would be increasingly prone to error as damage increased. We tested this by comparing estimates of damage from the template approach with the discrepancy in estimates between the two approaches. The significance of these correlations was tested using Spearman's correlation coefficients with a significance level of P?