Unfortunately, our pre-implant MR was acquired with double-dose gadolinium and we can't seem to extract the pial surface from it.
have you tried using bbregister to register post-op MRI with the pre-op surfaces? On Wed, 29 Oct 2014, Pierre M?gevand wrote: > 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 M?gevand, MD, PhD > PLOS Neuro Community editor - Follow us on Twitter > Postdoc @?Feinstein Institute for Medical Research (NY, USA) > Follow me on Twitter - Read my blog here > > 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 M?gevand > <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 M?gevand, MD, PhD > PLOS Neuro Community editor - Follow us on Twitter > Postdoc @?Feinstein Institute for Medical Research (NY, USA) > Follow me on Twitter - Read my blog here > > 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 M?gevand > <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 M?gevand > <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 M?gevand, MD, PhD > PLOS Neuro Community editor - Follow us > on Twitter > Postdoc @?Feinstein Institute for > Medical Research (NY, USA) > Follow me on Twitter - Read my blog here > <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. > -- 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>
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