Hi Daniel
I wouldn't advise this - you will miss most of the activation unless
it happens to be right next to where the surface runs adjacent to the
structure of interest. For subcortical structures you are better off
showing the results in slices.
cheers
Bruce
On Mon, 23
Feb 2015, Yang, Daniel wrote:
Hi Bruce,
Thanks for the reply. My main question is how to best visualize subcortical
activation in a figure.
Sometimes we do see some subcortical activation (like the attached, which
is a random search) (if the attachment does not work, please see the
examplehere:
http://www.frontiersin.org/files/Articles/18483/fnhum-06-00021-HTML/
image_m/fnhum-06-00021-g003.jpg).
Is it okay to visualize such subcortical activation via tksurfer? If not,
could you please recommend a method to visualize subcortical activation?
Sincerely,
Daniel
On 2/20/15, 9:06 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
HI Daniel
no, that won't work. Vol2surf samples a volume to an existig surface
and
none of the subcortical structures will be anywere near the cortical
surface. You would need to run mri_tessellate on each subcortical
label
that you want to generate a surface for, but I'm still not sure what
you
are trying to do.
cheers
Bruce
On Fri, 20 Feb 2015, Yang, Daniel wrote:
Hi Bruce,
Thanks! and yes, I used mri_vol2surf to convert subcortical
region as a
volume file to surface (mgh file) and then visualize it with
tksurfer.
According to what you said, this is still valid, right?
Best,
Daniel
On 2/19/15, 5:59 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Daniel
no, tksurfer visualizes surfaces exclusively, and the
subcortical
structures are volumetric by and large. You could
tesselate their surface
and view it in tksurfer, or just use tkmediit or freeview.
cheers
Bruce
On Thu, 19 Feb
2015, Yang, Daniel wrote:
Dear FreeSurfer experts,
I find that tksurfer allows me to visualize
subcortical areas such as
hippocampus. The
visualization looks valid to me.
Can tksurfer be used in this way?
Thanks!!
Daniel
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