Hi Ana,
Sorry I can't help more. Have never compared fsl and FS directly. Keep in mind that any consistent differences may also depend on the software version.
Maybe other people on the list have done some comparisons.
Best Martin
On May 26, 2012, at 13:59, Ana Arruda <anisabel.arruda@gmail.com> wrote:
> Thanks for your help Martin.
>
> However I don't have just a single subject with that discrepancy. My data has 18 subjects and most of the results obtained with Freesurfer are bigger than FSL.
>
> Thank you again,
>
> Ana
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