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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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