Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage.
Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to localize the electrodes, and a pre-implant MR scan to which we co-register the post-op exams and to whose smoothed outer pial surface we then "snap" the electrodes to, in order to account for the brain shift caused by the implantation procedure (Dykstra et al., 2012). Now, for one of our patients, the pre-op MRI was acquired with a lot of gadolinium, and we can't get Freesurfer to compute the pial surface. So I thought I would co-register the post-op exams to the fsaverage brain, and then snap the electrodes to fsaverage's outer smoothed pial surface as an approximation. Any idea how else I could do this? Thanks, Pierre On Oct 28, 2014 3:06 PM, "Marie Schaer" <marie.sch...@unige.ch> 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> > 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 > 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. > > >
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