That is not what Bruce is suggesting. Try to register the post-op to the pre-op using bbregister. You can then map the pre-op surfaces to the post-op brain
On 10/29/2014 01:58 PM, Pierre Mégevand wrote: > 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 > <mailto: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 <mailto: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 <mailto: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 <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 M?gevand > > <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 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 <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. > > > -- > 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> > > > _______________________________________________ > 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
