Hi Rashmi

why do you include $FREESURFER_HOME/FreeSurferColorLUT.txt on the command line? I think you can just remove it and you will be fine

cheers Bruce

On Wed, 1 Feb 2012, Rashmi Singh wrote:

While opening tkmedit using terminal I gave following command

% crick:~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer> tkmedit AA471.T0 brainmask.mgz -aux T1.mgz -segmentation aseg.mgz -surfs $FREESURFER_HOME/FreeSurferColorLUT.txt The output was Converting main surface: 100% done.        Converting main surface: 100% done.        Converting pial surface: 100% done.        Converting main surface: 100% done.        Converting main surface: 100% done.        Converting pial surface: 100% done.        LoadSegmentationVolume main aseg.mgz /opt/freesurfer/FreeSurferColorLUT.txt Reading /opt/freesurfer/tktools/tkm_common.tcl Reading /opt/freesurfer/tktools/tkm_wrappers.tcl Reading /opt/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /opt/freesurfer/tktools/tkUtils.tcl %

3 new windows popped up

1. The view window with the brain image ( it was similar to the one shown in you tutorial document-showed the surfaces and the segmentation in color)
2. The tool box window
3. Error message window stating the following

Error: Parsing arguments  Unrecognized option: /opt/freesurfer/FreeSurferColorLUT.txt  This option is not recognized by tkmedit.

Please explain what does this error message mean.

Rashmi.

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