Hello everybody,<br><br>I would like to ask you about the topology correction algorithm of freesurfer.<br>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.<br>

As I can see, the mris_fix_topology step requires the brain.mgz volume, but I am not sure how to produce it.<br><br>I have read the paper &quot;A METHODOLOGY FOR ANALYZING CURVATURE IN THE DEVELOPING BRAIN FROM  <br>PRETERM TO ADULT&quot; where the different tissues are substituted by uniform intensities recognised by freesurfer, but I would like to use the original image information if possible.<br>

<br>Is there any way to make use of the T1/T2 images (transform them) in the mris_fix_topology step?<br><br>Thank you very much for your time.<br><br>With kind regards,<br>Antonis<br>