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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
