Hi Pierre, Tricky question. So you can't really use the post-op cortical surface for this participant, right? Otherwise I would simply use the outer smoothed pial for this subject directly, which would be much more similar to the pre-op than the outer surface from the fsaverage (?). Otherwise, with the gadolinium MRI, maybe you can still get an adequate white surface, but I'm not sure that it would help you. The other option is to use the brain mask volume (which may work even with gadolinium if you are lucky, otherwise you can play with the watershed parameters), and tesselate a surface directly on this volume. But you'll get the two hemispheres at once (and probably the cerebellum as well), which may not be what you want?
Best, Marie On Oct 28, 2014, at 2:10 PM, Pierre Mégevand <pierre.megev...@gmail.com<mailto:pierre.megev...@gmail.com>> wrote: 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<mailto: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<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.
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