Hi Mallory,
TBSS uses FLIRT and FNIRT under the hood, so the results should be equivalent as long as you use the same flags. When calling FNIRT you probably want to use the configuration file for FA registration (--config=FA_2_FMRIB58_1mm). You might want to call the fsl_reg script directly, which is used in TBSS for the registration and calls FLIRT and FNIRT for you (with the appropriate flags if you use the -FA flag).
Calling fsl_reg or FLIRT/FNIRT will give you more flexibility than TBSS, but if you don't want to change any of the flags you could use TBSS as well.
Cheers,
Michiel
> On 6 Aug 2020, at 20:23, Mallory Kisner <[log in to unmask]> wrote:
>
> Dear FSL Experts,
>
> I have a group of subjects’ FA images that I am wanting to register to the MNI152 template so I can extract FA values for major tracts. From my understanding, I could do this by using FLIRT/FNIRT or I could run the first 3 steps of TBSS and use the target images for each subject. Am I correct in assuming I would get the same results with either method? If so, is there an advantage to using one method over another?
>
> Thank you in advance for your help!
>
> Mallory
>
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