It does not surprise me that it fails on the fsaverage surface. I agree with Marie that it is not good idea to use LGI on fsaverage for anything. Definitely not its intended purpose. doug
On 10/28/2014 03:06 PM, Marie Schaer wrote: > > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
