don't rerun that as it will rerun the surface deformation. Use mris_thickness and mris_curvature
On Sun, 11 May 2014, S.V.Shepherd [work] wrote:
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.shepherd@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? stephenstephen 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 fischl@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 <fischl@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
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