what hardware are you running on? We can send you a version of mris_copy_header. Or you can can send me the two surfaces (before and after smoothing) and I can see if it fixes the problem
cheers Bruce On Thu, 10 Dec 2015, Chris Holdgraf wrote:
Yep - sorry, here's apic: https://cloud.githubusercontent.com/assets/1839645/11702154/263fb152-9 e89-11e5-8485-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 fischl@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 <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 > _____________________________________ > > _______________________________________________ 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 Editor and Web Director | Berkeley Science Review _____________________________________
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