HI SCT team,
I wasn’t able to reply to the existing ticket on sourceforge, so will carry on here instead 
The plot thickens…please bear in mind that I’ve always used the viewer to supply the center line of the spinal cord, but just for kicks I tried running deepseg without the viewer, instead letting it use the default svm method.
sct_deepseg_sc -i sanlm_structural.nii.gz -c t1 -ofolder deepseg
which I wanted to compare to my standard call:
sct_deepseg_sc -i sanlm_structural.nii.gz -c t1 -ofolder deepseg.viewer -centerline viewer
In short, selecting the centre of the cord (really really carefully) makes deepseg fail. See attached.
RED = deepseg automatic, BLUE = deepseg with viewer selected center line (+ overlap for comparison). (Please note: I’ll have to post the images in separate replies)
Hope this helps - I will send Julien a link to the data set - but please note this is not specific to just this subject - I see this behaviour consistently.
Best wishes,
Jon
