Hi Evan

how big is that defect? The topology correction complexity goes as the square of the convex hull of the largest defect, so fast for small ones but a long time for big ones. Usually big ones only occur if there is something seriously wrong though (e.g. skull attached to the white matter)

cheers Bruce On Thu, 3 Feb 2011, Evan Luther wrote:

Hello,

My name is Evan Luther and I have been working with Dr. David Ress at the University of Texas at Austin to create a high resolution (.7 mm) volume using FreeSurfer. In the last step of our data pipeline I enter the command:

recon-all -segmentation -fill -tessellate -smooth1 -inflate1 -qsphere -fix -smooth2 -inflate2 -finalsurfs -cortribbon -s fsHighRes

After running for several hours this reconstruction gets stuck in the mris_fix_topology command. This command does not have much documentation on the FreeSurferWiki although from what I understand it is ensuring that the cortical surface is topologically correct. It picks out about 216 topological errors and gets stuck on the 93rd. I left it running on this error for quite some time (>24 hours) and nothing occurred.

Can anyone offer me any insight or help?

Thank you very much,

Evan Luther