Thanks Nick,

That did it. Can I update the wiki page with this change?

Cheers,

-Morgan

Nick Schmansky wrote:

This should work:

tkmedit good_output brainmask.mgz \ lh.white -aux T1.mgz \ -aux-surface rh.white \ -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt

On Thu, 2007-04-12 at 16:54 +0100, Morgan Hough wrote:

...

I have a quick question about an error we are getting with FS 3.0.5 when we are using tkmedit as described in the tutorial to display the segmentations overlaid on the T1.

tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz

The first error seems to regard the new requirement that a color LUT be passed with the segmentation option. If we add

tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz tkmeditColorsCMA

Then the message reduces to a problem of opening the segmentation file which it says is not in the right .cor format. I assume this is a legacy error message but I am not sure if I need to rename the aseg.mgz file or pass in another option with the file type.

Thanks in advance for your time.

Cheers,

-Morgan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi,

I just want to clear up some confusion about this topic. There is a difference currently between the dev (and stable) versions within the Martinos Center and versions that have been posted for download.

Some versions will require you to specify a color table, and also to use the mri/ designation before the aseg.mgz file name.

Other versions will not need (and fail if you use) the mri/ designation before the aseg.mgz filename. These versions do not need a color table, as it will read one in by default.

It makes the most sense (to me) to continually update the wiki pages to be current with the newest versions, so there are times when certain commands may not be the same as your version - generally nothing drastic.

Sorry for any confusion the current documentation has caused. Jenni

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Doug Greve Sent: Monday, April 16, 2007 7:16 PM To: Nick Schmansky Cc: Morgan Hough; Freesurfer Mailing List Subject: Re: [Freesurfer] aseg visualization question

Newer (dev) versions will use $FREESURFER_HOME/FreeSurferColorLUT.txt as the default.

On Thu, 12 Apr 2007, Nick Schmansky wrote:

This should work:

tkmedit good_output brainmask.mgz \ lh.white -aux T1.mgz \ -aux-surface rh.white \ -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt

On Thu, 2007-04-12 at 16:54 +0100, Morgan Hough wrote:

...

I have a quick question about an error we are getting with FS 3.0.5 when we are using tkmedit as described in the tutorial to display the segmentations overlaid on the T1.

tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface

rh.white -segmentation aseg.mgz

...

The first error seems to regard the new requirement that a color LUT be passed with the segmentation option. If we add

tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface

rh.white -segmentation aseg.mgz tkmeditColorsCMA

...

Then the message reduces to a problem of opening the segmentation file which it says is not in the right .cor format. I assume this is a legacy error message but I am not sure if I need to rename the aseg.mgz file or pass in another option with the file type.

Thanks in advance for your time.

Cheers,

-Morgan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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