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. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- _____________________________________ PhD Candidate in Neuroscience | UC Berkeley <http://hwni.org/> Editor and Web Director | Berkeley Science Review <http://sciencereview.berkeley.edu/> _____________________________________
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