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
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