Hello everybody,
I would like to ask you about the topology correction algorithm of freesurfer. I have produced the tissue segmentation for a number of neonatal brains, but as they are not topologically accurate, I would like to try your algorithm to fix the surfaces. As I can see, the mris_fix_topology step requires the brain.mgz volume, but I am not sure how to produce it.
I have read the paper "A METHODOLOGY FOR ANALYZING CURVATURE IN THE DEVELOPING BRAIN FROM PRETERM TO ADULT" where the different tissues are substituted by uniform intensities recognised by freesurfer, but I would like to use the original image information if possible.
Is there any way to make use of the T1/T2 images (transform them) in the mris_fix_topology step?
Thank you very much for your time.
With kind regards, Antonis