[Freesurfer] Freesurfer and FSL

Dear experts,

I'm an MSc student and part of my final project is related to the measurement of the volume of the hippocampus. The last thing I have to do is to compare two softwares, FSL and Freesurfer.

On Freesurfer, I've used the following commands:

recon-all -i where_my_subject_is -autorecon1 -s output_name

then, related to the same subject

recon-all -autorecon2 -s output_name

After approximately 12 hours, and after comparing the results of Freesurfer and FSL, I found that those obtained with Freesurfer are bigger than those obtained with FSL. According to the literature the results are the reverse.

Do you know any idea what I'm doing wrong?

Thank you for your attention,

Ana Arruda