Hi Caroline

the colortables are in $FREESURFER_HOME. Usually we use

$FREESURFER_HOME/FreeSurferColorLUT.txt

cheers Bruce

On Mon, 1 Aug 2016, Caroline Beelen wrote:

Dear FS,

Sorry to bother again, but I’m currently in need for some quick help.

Today, I also ran into another problem. I tried to display only few ROI’s in Freeview instead of the whole brain. Therefore, I tried to create a new annotation file consisting of only few labels (from regions of DK-atlas) and I used the mri_annotation2label on my own created fsaverage to get these labels. This worked fine.

Then I used the command of mris_label2annot to create the annotation file, but part of the command, --ctab aparc.annotation.ctab, is not recognized. Replacing it by –ctab  fsaverage/label/lh.aparc.annot (file exists in the label folder of fsaverage) gives me the following error: CTABreadASCII: badly formed file. ERROR: reading fsaverage/label/lh.aparc.annot. I couldn’t find, or create, any other aparc.annot file.

What would be the right command (for the part of ctab) to get mris_label2annot working? Or is there perhaps a better way to only display certain ROI’s in Freeview? (the latter I could still explore but assistance is certainly appreciated)

Thanks a lot!

Caroline