CC values all 0 in aseg+DKT.stats

[karllandheer]

Hello, attached is a screenshot of an aseg+DKT.stats file I have. As you can see, the CC values are all 0. I assume I am doing something wrong? Any ideas?

[m-reuter]

maybe. What is the command you ran? The CC is added later in the recon-surf pipeline, but there is an option to stop after CC is added and not run the full surfaces.

[karllandheer]

Hello, sorry I should have included it. This is the line I have used to run it:

docker run -v ${SETUP_DIR}:/data my_fastsurfer:cpu \
   --t1 /data/T1_unbiased_brain.nii.gz --sd /data/  --sid Tutorial \
   --py python3 --allow_root --3T  --fs_license /data/FreeSurferLicense.txt \
   --parallel --fsaparc --threads 2

[m-reuter]

Thanks, looks good. So I check the readme and the aseg+DKT.stats file gets created directly after the segmentation, so it will not yet contain the CC. You should look e.g. at the aseg.stats for that.

[m-reuter]

Did you find the CC values in aseg.stats? I will close this now. Feel free to re-open if those values cannot be found there.

[karllandheer]

Hello, yes it is there. Thank you for the great support!!