The weird thing (given your description) is that I was in fact seeing the label names in tkmedit (e.g., "wm-ON"), even though that information is not in FreeSurferColorLUT.txt. So, it appears that perhaps 'tkmedit' is indeed set-up to read the labels that are embedded in the edits.mgz file...?
thanks, -MH >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 >> >> > > > > 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
