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 >> >
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