Hi FS Experts,

I’m having trouble getting anatomical stats from a parcellation I made out of scanner-space volume ROIs.  I have taken the following steps to do this.

  1. mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o myROI_orig.nii.gz --interp nearest
  2. mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct ROI_test_table.txt 
    1. On this step I ALWAYS get an error “could not open translation file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt” even though I specify a CT with -ct, or when I specify a table with -t, or with both
    2. This seems to work though and I can view this annot on the surface with tksurfer
  3. mris_anatomical_stats -a /path/to/myROIs.annot -b Subj111 lh


When I run mris_anatomical_stats I get the following error: 
CTABfindAnnotation: ct was NULL
Segmentation fault (core dumped)

I’m guessing this is from the color-table not being embedded in the annot file, but I’ve tried to get that embedded in many ways.  

My questions are:

  1. What is causing the error with mris_anatomical_stats?
  2. What is the difference between the -t and -ct flags for mris_sample_parc and which should I use?
  3. Should I use a specific color-table for this?  I made my own which was just a space delimited file with “index name r g b a” for all my ROIs, but should I be adding this data to some existing color-table to make this work?

Thanks,
Jared