Thanks Christopher for your answer.
First of all, I want to run the step tbss_non_FA in the data of MD,RD and AD. To do that at the website of fsl (tbss user guide) is explained that you have to copy your data into a new file (for example copy dti_L1 file of all my patients into a file called AD) to run the tbss steps into this file, in order to analyse AD,MD,RD data.
The images of all_MD, all_AD and all_RD that I had when I run tbss steps in MD,RD and AD images were very ugly like a mess of black and white without any structure visible.
However, when I copy all my dti_L1 images (AD file) directly into the file where before I had run tbss steps of dti_FA (this file contains origdata,FA and stats)and I run the script tbss_non_FA AD into this directory, the results are good, the image of all_AD is clear and is not a mess like the other one.
Maybe I misunderstood the steps of tbss_non_FA analysis.
Thanks!
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