My name is Flavio, student at Universidade Federal Fluminense. I research image segmentation methods applied to brain cortical structures segmentation.

I’ve compared against the hippocampal region got from FIRST-FSL to Freesurfer, using the same magnetic resonance (MR) image.

The FSL is a neuroimage analysis tool developed  by FMRI group from Oxford. I found out a great volume difference between segmentations. Despite different automated image analysis tool,  I was expecting a higher volume overlap index when comparing the same brain structure from the same MR image. I got about 25% volume overlap.

Is there any “recon-all” flag that I can use in conjunction with entire process so as to get better volume overlap? I would appreciate any suggestion.

Thank you in advance,

Flavio.