Mike, thanks for pointing out that bug, i've fixed it for the next release.
per the edits.mgz, i see now that the colortable should be printed when mri_compile_edits is run (actually, its embedded in the edits.mgz file, but tkmedit is not setup to read it). so this is the table it ought to print, and if you save these lines in a file, you can include that filename just after the edits.mgz param in the tkmedit command and it will load that table (instead of the default FreeSurferColorLUT.txt) : 0 Unknown 0 0 0 0 1 wm-OFF 0 0 255 0 2 wm-ON 255 0 0 0 3 brain-OFF 0 255 255 0 4 brain-ON 255 255 0 0 5 brainmask-OFF 0 64 255 0 6 brainmask-ON 255 26 0 0 7 brain.finalsurf-OFF 0 128 255 0 8 brain.finalsurfs-ON 255 128 0 0 9 aseg-CHANGED 255 255 128 0 N. On Tue, 2012-01-31 at 12:38 -0600, Michael Harms wrote: > Hi Nick, > > I found a small bug in recon-all that prevents the -showedits flag from > working in conjunction with expert-options: > > Line 785 in recon-all of v5.1 currently has an extraneous closing > parenthesis: > if (-e $XOptsFile)) then > > but should be: > if (-e $XOptsFile) then > > Also, I'm puzzled how the resulting edits.mgz gets translated when you > load it as a segmentation -- e.g., areas with an addition to wm.mgz > appear to be assigned the value 2 in edits.mgz, and are labeled as "wm- > ON" if you load edits.mgz as a segmentation, but I don't see any entry > for "wm-ON" in FreeSurferColorLUT.txt itself. Where is the full "key" > for the values in edits.mgz? > > thanks, > -MH > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ 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.
