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 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 <[email protected]>
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
<[email protected]> 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 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
<[email protected]> 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
<[email protected]>
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"
<[email protected]> 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
<[email protected]> 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 editor - Follow us
on Twitter
Postdoc @ Feinstein Institute for
Medical Research (NY, USA)
Follow me on Twitter - Read my blog here
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