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<<FslToolContents>>
= Step by Step Guide =
== TBSS (voxel-wise analysis of local diffusion measures) ==
 * Do a tensor fit with [[FDT/StepByStep|DTIFIT]]
 * Make a directory for the analysis
 * Copy the FA images into this directory
 * ''Standard'' [[TBSS/UserGuide|TBSS]] analysis (of FA):
   * `tbss_1_preproc *.nii.gz`
   * `tbss_2_reg -T`   (recommended - one registration per image, deriving a study-specific template)
       * alternative is to use a custom template (-t)
       * use best target from all images (-n) - lots of registrations
   * `tbss_3_postreg -S`   (-T for FMRIB58)
       * view/check the skeleton output
   * `tbss_4_prestats 0.2`
   * `cd stats`
   * Use the Glm GUI to create appropriate design matrices and contrasts, and save the design
   * Run [[randomise]] with the design files from the Glm GUI and appropriate multiple-comparison correction (e.g. `--T2`)
 * View the results
   * look at the *corrp* images (these are the multiple comparison corrected p-values, stored as 1-p values)
   * tbss_fill for making a thicker skeleton for more easy viewing and creating figures for publications