I’m trying to switch from using sct_propseg command for cord segmentation to the deepseg command but it keeps giving me an error message.
I’ve tried many different combinations but in general this is what I was working with: sct_deepseg_sc -i t2.nii -c t2 -qc $qc but it always gives me: argument -qc: expected one argument, and won’t let me proceed. If you have any advice I would greatly appreciate it as I would prefer to collect my data using the deepseg command. Recently updated to 5.8.
Thank you!
My first suggestion would be to try the command again, but this time putting double-quotes around the $qc part:
sct_deepseg_sc -i t2.nii -c t2 -qc "$qc"
I can only guess (because I don’t know the value of you $qc that you are using), but my hunch is that the $qc variable contains a space in it somewhere. (Perhaps a folder somewhere in the QC path has a space?)
If this is true, then without double-quotes, $qc will be interpreted as two separate arguments, split in two where the space is. So, by adding double-quotes, we can make sure that $qc will be treated as a single argument.
If this doesn’t work, could you please share the value of $qc so I can help you debug further?
