It's a cluster running Linux CentOS 64-bit. If it's as simple as getting
the file and adding it to my path I'm happy to give it a try...
Chris
On Thu, Dec 10, 2015 at 1:47 PM, Bruce Fischl
wrote:
> what hardware are you running on? We can send you a version of
> mris_copy_header. Or you can can
what hardware are you running on? We can send you a version of
mris_copy_header. Or you can can send me the two surfaces (before and
after smoothing) and I can see if it fixes the problem
cheers
Bruce
On Thu, 10 Dec 2015,
Chris Holdgraf wrote:
Yep - sorry, here's apic:
https://cloud.github
Yep - sorry, here's a pic:
https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9e89-11e5-8485-dc97c8ca2ca7.png
You can see the smoothed version is shifted lower.
I couldn't find mris_copy_header on my path. Is it only included in the
beta version? I'm running 5.3. Could try beta
and how do you determine they are shifted? In freeview? The surface
geometry/position should be preserved in the smoothing but appears to not
to be. Perhaps Marie can comment? Or you can try mris_copy_header to see if
that does the trick
cheers
Bruce
On Thu, 10 Dec 2015,
Chris Holdgraf wrot
Hey Bruce - thus far I have used pretty default parameters. I first ran
recon-all on each subject, then simply ran `recon-all -s s_name -localGI`.
Here are the transforms for the original vs. inflated surface
On lh.pial:
talairch.xfm:
1.103 0.015 -0.002 4.202;
-0.032 1.064 0.063 -19.65
Hi Chris
how do you smooth the surface? Are you sure that you retain the surface
header information? Try looking at the header with mris_info before and
after smoothing
cheers
Bruce
On Thu, 10 Dec 2015, Chris Holdgraf wrote:
> Hey Freesurfer folks - I'm looking into using Freesurfer for doing
Hey Freesurfer folks - I'm looking into using Freesurfer for doing
electrode reconstruction / co-registration in electrocorticography. We're
making good progress on figuring out recon-all for surfaces and doing
co-registration to CTs. However, I think I've encountered a strange bug.
I'm trying to
