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

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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" mharms@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

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