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. > >
_______________________________________________ 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.
