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 ju
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 el
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,
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
Is the corpus callosum segmentation based on the Hofer and Frahm functional
parcellation, a mathematical formula, or, as listed on the website, 5 equal
subdivision roughly along the long axis? What is the preferred citation for
this?
Thanks.
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Freesurf
It does not surprise me that it fails on the fsaverage surface. I agree
with Marie that it is not good idea to use LGI on fsaverage for
anything. Definitely not its intended purpose.
doug
On 10/28/2014 03:06 PM, Marie Schaer wrote:
>
> Hi Pierre,
>
> I'm not sure exactly what you are trying to
Hi Maria,
Here are the responses:
1. Can you send us a screenshot of what you mean with "it doesn't hug the
contours of the brain mask"? You can use: tkmedit T1.mgz lh.pial
-aux-surface lh.pial-outer-smoothed (or the corresponding in freeview) and it
should give you what correspond to the to
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 ca
glad to hear it
Bruce
On Tue, 28 Oct 2014, Smith, Michael wrote:
> Hey Bruce,
>
> Never responded but this worked out great thanks for the help.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fisch
Hey Bruce,
Never responded but this worked out great thanks for the help.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, October 23, 2014 9:31 AM
To: Freesurfer support list
Subject
Hello,
I am interested in using functional data collected from 7t using freesurfer
and fsfast. We would like to use EPI field maps to warp this data to 3T
anatomical space. Can anyone guide me as to how to do this.
Best,
B
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Free
sounds good
Bruce
On Mon, 27 Oct 2014, Adam Mezher wrote:
Hi Bruce,
I performed both cp and wm edits and was able to fix most of the subjects in
the meantime. I’ll still see if I can get it ftp’d over to you guys to take
a look for future reference.
thanks!
Adam
Hi Adam
it's impossible
Hi Doug,
For some reason, I no longer get an e-mail when you respond to my questions
on the mailinglist, so until today I only saw the first response to this
question (from Bruce).
Anyway, I get your point about smoothing and clusters but I guess showing a
continuous cortical map with vertex valu
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