Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks "cut". It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from.
But in any case, I wouldn't advice to run the LGI on the fsaverage, as the pattern of cortical folding is lost from the averaging of the subjects. So I'm not even sure that the algorithm will work even if you get mris_fill to work. Can you tell us more precisely what you are trying to do? And why on the fsaverage rather than on your individual subject? Best, Marie On Oct 28, 2014, at 5:31 AM, Pierre Mégevand <pierre.megev...@gmail.com<mailto:pierre.megev...@gmail.com>> wrote: Dear all, I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after a good while. More importantly for me, the lh.pial-outer-smoothed surface, which I am after, did not look right. It seems that the first step, mris_fill, produces a volume that does not look very much like a brain anymore (cf. attached screenshot). Any idea why that would happen? Thanks, Pierre -- Pierre Mégevand, MD, PhD PLOS Neuro Community<http://neuro.plos.org/> editor - Follow us on Twitter<http://twitter.com/PLOSNeuro> Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter<http://twitter.com/pierre_vanmedge> - Read my blog here<http://neuroscimed.wordpress.com/> <screenshot3.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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.
_______________________________________________ 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.
