i guess all thats needed then is for -showedits to print the table (which it does now, for the next release) and for mri_info to show the table if its embededed (i'll add that).
N. On Tue, 2012-01-31 at 22:02 -0500, Bruce Fischl wrote: > 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
