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 <fis...@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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_____________________________________
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Editor and Web Director | Berkeley Science Review
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