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.
mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o
myROI_orig.nii.gz --interp nearest
mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct
ROI_test_table.txt
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
This seems to work though and I can view this annot on the surface with tksurfer
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:
What is causing the error with mris_anatomical_stats?
What is the difference between the -t and -ct flags for mris_sample_parc and
which should I use?
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
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