Yep - sorry, here's a pic: https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9e89-11e5-8485-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 <fis...@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 < >> 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 >> > _____________________________________ >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. 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