Dear SCT experts,
I am facing a problem while using the command sct_register_to_template.
I just call the command like this: sct_register_to_template -i T2.nii.gz -s T2_seg.nii.gz -ldisc T2_seg_labeled_discs_edited.nii.gz I created the labeled_discs by using sct_label_vertebrae command (which work quite well). I have 8 labels in this nifti file (from 2 to 9).
When I run the command I get the following error:
Straighten the spinal cord using centerline/segmentation…
Create temporary folder (/tmp/sct-20190903104329.637122-straighten_spinalcord-etincqvm)…
Copy files to tmp folder…
Create the straight space and the safe zone
Length of spinal cord: 134.47821556475964
Size of spinal cord in z direction: 127.99999999985897
Ratio length/size: 1.0506110591008422
Safe zone boundaries (curved space): [-86.1999969487103, 41.80000305114868]
Safe zone boundaries (straight space): [-89.43910473116063, 45.03911083359901]
Traceback (most recent call last):
File “/home/willi/sct_4.0.1/scripts/sct_register_to_template.py”, line 871, in
File “/home/willi/sct_4.0.1/scripts/sct_register_to_template.py”, line 437, in main
File “/home/willi/sct_4.0.1/spinalcordtoolbox/straightening.py”, line 218, in straighten
centerline_straight = _get_centerline(image_centerline_straight, algo_fitting, self.degree, verbose)
NameError: name ‘algo_fitting’ is not defined "
When I just give one label instead of 8, function runs without any errors.
Before switching to 4.0.1, I was using 4.0.0- beta 5 and I did not have this problem.
Should I straighten the cord first, and then use this as an input ?
Thanks a lot!