Hi Michael,
thanks a lot for the reply! I went through all of TBSS and created an all_FA_skeletonised.nii image. Then I created a ROI using the WM Atlas and I was thinking of using fslmeants on the ROI over the all FA skeletonised. Would this yield me a similar result or would be using fslstats better?
Thanks!
Dragana
> On 13. Jun 2020, at 15:16, Michiel Cottaar <[log in to unmask]> wrote:
>
> Hi Dragana,
>
> You can extract the average FA values across the ROI using fslstats.
>
> Note that if you are interested in getting average ROI values in the tracts, it might be good to run through all of TBSS, so that you get the individual's subjects FA values projected onto the skeleton. You can then compute the average FA values for each white matter ROI only on the white matter skeleton, which will be much less affected by partial voluming than if you use the full ROI.
>
> Best wishes,
>
> Michiel
>
>> On 13 Jun 2020, at 10:44, Dragana Galevska <[log in to unmask]> wrote:
>>
>> Hi,
>>
>> I am planning to do something similar so this would interest me too.
>> BTW, are you then planning to do ROI analysis on the FA maps and extract the FA values from the chosen ROI?
>> And would you know if there is a pipeline for this?
>>
>> Good luck!
>>
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