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.githubusercontent.com/assets/1839645/11702154/263fb152-9
e89-11e5-8485-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 as well, just not sure how stable
it is...
On Thu, Dec 10, 2015 at 12:38 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
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 wrote:
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 -19.651;
0.015 -0.008 1.170 -25.227;
0.000 0.000 0.000 1.000;
surfaceRAS to talaraiched surfaceRAS:
1.103 0.015 -0.002 4.752;
-0.032 1.064 0.063 -15.999;
0.015 -0.008 1.170 1.733;
0.000 0.000 0.000 1.000;
talairached surfaceRAS to surfaceRAS:
0.906 -0.013 0.002 -4.519;
0.028 0.939 -0.051 14.976;
-0.012 0.007 0.854 -1.320;
0.000 0.000 0.000 1.000;
volume geometry:
extent : (256, 256, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : (-1.0000, 0.0000, 0.0000)
y_(ras) : ( 0.0000, 0.0000, -1.0000)
z_(ras) : ( 0.0000, 1.0000, 0.0000)
c_(ras) : ( 0.5078, 2.0802, 23.0431)
On lh.pial-outer-smoothed:
talairch.xfm:
1.103 0.015 -0.002 4.202;
-0.032 1.064 0.063 -19.651;
0.015 -0.008 1.170 -25.227;
0.000 0.000 0.000 1.000;
surfaceRAS to talaraiched surfaceRAS:
1.103 0.015 -0.002 4.202;
-0.032 1.064 0.063 -19.651;
0.015 -0.008 1.170 -25.227;
0.000 0.000 0.000 1.000;
talairached surfaceRAS to surfaceRAS:
0.906 -0.013 0.002 -4.011;
0.028 0.939 -0.051 17.057;
-0.012 0.007 0.854 21.723;
0.000 0.000 0.000 1.000;
volume geometry info is either not contained or not
valid.
---
I highlight that last bit because maybe it's
important? Looks like some
information goes missing in there...
Chris
On Thu, Dec 10, 2015 at 10:27 AM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
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 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 create a smoothed pial surface
so that I project
electrodes
> onto this surface. The code seems to run
correctly, however,
the smoothed
> surface looks translated relative to the
original pial surface
that it was
> created from.
>
> For example, see this issue I opened on
github:
>
> https://github.com/aestrivex/gselu/issues/7
>
> Anyone have an idea why this is happening?
I'm not sure why
the pial surface
> would be correct, while the smoothed surface
would be shifted.
>
> Chris
>
>
> --
> _____________________________________
>
> PhD Candidate in Neuroscience | UC Berkeley
> Editor and Web Director | Berkeley Science
Review
> _____________________________________
>
>
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