Looking over our scripts, it appears we normally generates the surfaces etc. through recon-all -autorecon2-wm <...> -noaseg despite that ?h.pial isn't explicitly listed as an output in the dev table ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable).
It looks like a step from autorecon3 might be useful: mris_make_surfaces <subjID> ?h -orig_white ?h.orig orig_pial ?h.pial to update the curvature and thickness files without changing the wm and pial -- but I'm not sure this is how it works. stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Sun, May 11, 2014 at 5:22 PM, S.V.Shepherd [work] < stephen.v.sheph...@gmail.com> wrote: > Hi Bruce, > > How would I go about updating the thickness estimates (?h.thickness, I > presume) after manually adjusting the pial surface in FreeView? Are the > other surfaces (inflated, sphere, etc.) unaffected by this change, or > should they be recalculated as well? > > stephen > > *stephen v. shepherd phd* > The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA > // 212.327.7620 > > > On Sun, May 11, 2014 at 3:51 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu>wrote: > >> Hi Stephen >> >> only the thickness estimates should matter, unless you've lost an entire >> gyrus or something >> >> Bruce >> >> On Sun, 11 May 2014, S.V.Shepherd [work] wrote: >> >> Hi Bruce, >>> >>> This is the manual edit of the pial surface in FreeView, correcting >>> locations where the grey >>> matter failed to grow out of the white matter. It took place after the >>> pipeline had >>> completed, but I'm not sure if I need to rerun/regenerate steps which >>> are dependent on the >>> pial surface. For example, are mris_sphere, mris_curvature, and >>> mris_flatten dependent upon >>> the pial surface or cortical thickness, or do they work directly off the >>> wm/orig surface? >>> If the former, I should rerun them; if the latter I don't need to do >>> anything but just >>> repaint the functional statistics of interest using mri_vol2surf and the >>> updated cortical >>> bounds (which I presume happens automatically, having corrected ?h.pial). >>> >>> My comment about morphometry was meant to note that, since I'm manually >>> changing the >>> distance between the wm and pial surface in places where there were >>> medial surface >>> artifacts, it would be unwise to try to draw any conclusions from >>> comparing >>> manually-adjusted and automatically-calculated cortical thicknesses. >>> >>> stephen >>> >>> >>> >>> >>> stephen v. shepherd phd >>> The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 >>> USA // 212.327.7620 >>> >>> >>> On Sun, May 11, 2014 at 9:50 AM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> wrote: >>> Hi Stephen >>> >>> why do you say it invalidates the morphometry? And we need to know >>> what pial >>> surface editing you did in order to answer your questions (and >>> what recon-all >>> steps you rerean) >>> >>> cheers >>> Bruce >>> >>> >>> On Sun, 11 May 2014, S.V.Shepherd [work] wrote: >>> >>> Hi Bruce, >>> >>> Thanks again for your help at the FreeSurfer course. I've >>> corrected >>> the pial surface >>> manually (knowing that this invalidates the morphometry, but >>> that by >>> restoring the medial >>> surface it does let me process functional data). Having >>> done this, >>> do I need to remake >>> spheres and patches, or are these unchanged? For example, >>> when >>> using mri_vol2surf, does >>> freesurfer know what elements to sample by consulting the >>> ?h.orig >>> and ?h.pial, or are there >>> downstream files I should update as well? >>> >>> Thanks! >>> >>> stephen >>> >>> >>> >>> >> _______________________________________________ >> 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. >> >> >
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