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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Editor and Web Director | Berkeley Science Review
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