Hi @Stefan_Radonjic ,
So, I confirm that the default
sct_propseg commands fails with the default parameters. The key for a robust segmentation is to pass a proper centerline. This could be achieved with
sct_deepseg_sc, which segments the cord, and that segmentation could be used as an input centerline to
# Segment cord with deepseg
sct_deepseg_sc -i MR_frame_0001.nii.gz -c t2 -centerline svm
# Segment CSF with propseg.
# Note: we specify an output folder in order to avoid overwritting the already existing cord segmentation
sct_propseg -i MR_frame_0001.nii.gz -c t2 -init-centerline MR_frame_0001_seg.nii.gz -CSF -ofolder propseg
Here is the output segmentation of the cord (red) and CSF (blue):
Note that the CSF segmentation doesn’t go all the way. You might want to play with the propseg parameters to improve this, but at least now you have a good starting point.