Our usual method for electrode localization remains in the patient's space: co-register post-op MR and CT with pre-op MR brainmask (our reference space) and snap electrodes to patient's outer pial surface.
My idea was: register the patient's (crappy) brainmask volume to the "Talairach" fsaverage volume (not surface), which I can correct manually; use the Talairach.xfm transform to bring the electrodes into that same fsaverage volume, and then snap the electrodes to fsaverage's outer pial surface. But that last step I can't perform. I'm aware that the localization would be pretty inaccurate. I'll look into what you suggest Marie. In case all else fails, the last resort is to show the actual post-op MR and CT slices for electrodes of interest, but that just does not look as appealing as pial surfaces! -- 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> On Wed, Oct 29, 2014 at 12:29 AM, Marie Schaer <marie.sch...@unige.ch> wrote: > > So what I don't get in your pipeline is how you'll register the post-op > brain to fsaverage if you don't have any cortical surface in the post-op? > > If I were you, if you want precise registration that includes the sulci, > I'd go with the white surface from the pre-op gadolinium scan. And if you > just want a rough registration of the skull shape, then you can probably > find a way to create the outer surface directly on the gadolinium scan: if > your brain mask is good, then mris_fill should work (maybe you need to > binarize the data first (in any case a few lines of code in matlab should > do the trick). If the brain mask is not good due to gadolinium, then either > playing with mri_watershed (and maybe try mri_fill to separate the > hemispheres / pons and cerebellum) and then mris_fill for the tessellation. > Or if it doesn't work with mri_watershed, playing a bit with threshold with > another skull-stripping program (e.g. MRIcro), then importing the volume > back in FreeSurfer and use mris_fill to get a good tessellation. Both > solutions will need you to play a bit, but I guess you cannot really afford > to simply throw these data and take another subject! > > Good luck, > > Marie > > > > On Oct 28, 2014, at 2:57 PM, Pierre Mégevand <pierre.megev...@gmail.com> > wrote: > > You're right, we can't use the post-op surface because of the > deformation caused by surgery and the electrode artifacts. > > Getting a surface right from the brainmask would be OK, if we can't get > anything better, but the nice thing about using the fsaverage surface is > that you can plot and compare electrode locations from multiple patients. > Just in case we have nothing better, though, how would you do it? > > Thanks again! > > -- > 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/> > > On Tue, Oct 28, 2014 at 5:23 PM, Marie Schaer <marie.sch...@unige.ch> > wrote: > >> >> 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> >> 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> 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. >>> >>> >>> >> > >
_______________________________________________ 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.
