Comments (5)
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.
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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
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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.
from fastsurfer.
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.
from fastsurfer.
Hello, yes it is there. Thank you for the great support!!
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Related Issues (20)
- Support for lesion masks? HOT 1
- Unmatched ROIs in predicted segmentation and provided FastSurfer_ColorLUT.tsv HOT 23
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- ERROR: FastSurfer asegdkt segmentation failed. HOT 8
- Surface module fail in dev HOT 6
- Reference to deprecated docker images in surface pipeline docs HOT 5
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