I think the .mgz format supports an embedded color table
On Jan 31, 2012, at 9:52 PM, "Michael Harms" <mha...@conte.wustl.edu> wrote: > > 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
