Hi Antonis,
you can try running it with the T2 as the brain.mgz and see how it goes. We do this fairly routinely on ex vivo data (which is T2* weighted) and it does ok. Not as well as in vivo where the contrast is what we expect, but it does produce topologically correct and geometrically reasonable surfaces.
cheers Bruce On Tue, 28 Jun 2011, Antonis Makropoulos wrote:
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