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Hi freesurfer experts,

I'm trying to extract mean FA values (dti_FA.nii.gz) using a segmentation 
volume (parc2502dwi.nii.gz) and the corresponding color table with:

for subj in SPN01*; do
    if [ -d "${subj}" ];
    then
        cd $subj/
        # extract FA
        mri_segstats \
                 --seg mri/parc2502dwi.nii.gz \
                --ctab colortable.txt \
                 --i $dtipath/$subj/dti_FA.nii.gz \
                 --excludeid 0 \
                 --sum ../FA/${subj}_fa.stats
        cd ../
    fi
done

The color table has 297 parcels specified but the summary statistics file only 
includes 38 regions. This is due to zero values in the other regions, I assume.
Both (dti_FA and parc2502dwi) are perfectly co-registered.

Not providing a color table results in 1234 regions being read out.

Am I missing an argument in my command?
Or is there anything else that is obviously wrong?

I would be very glad for some hints!

Thanks,
Steph


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