Hi - I'm a bit confused - it sounds like you're pre-replicating some of the TBSS steps - the TBSS scripts themselves run FLIRT and FNIRT, so you don't have to (and shouldn't) before running TBSS - just feed in the "raw" dtifit-output FA images.

Cheers.

On 30 Sep 2014, at 14:03, M. alshikho <[log in to unmask]> wrote:

Hi FSL Experts,
I want to run TBSS for my 40 subjects (20 controls 20 patients).
Is it correct if I did FLIRT and FNIRT for every FA map then use the FLIRTED_FNIRTED FAmaps in TBSS scripts.
Is this procedure correct? Is it able to increase the sensitivity of TBSS or just it will add more bias to the final results?

Thanks
Mohamad

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