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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