I ran the sct_label_vertebrae on a t2w file using a seg file created using deepseg -

things appear to be processing routinely (output attached) - but after a minute or so - I get the following error:

```
(sct-env) david@ubuntu-work-vm:/mnt/workspace/sct_june2019/sct_dev/sub-ID03/anat$ sct_label_vertebrae -i sub-ID03_T2w.nii.gz -s deepseg/sub-ID03_T2w_seg.nii.gz -c t2
--
Spinal Cord Toolbox (dev)
Create temporary folder (/tmp/sct-20190911102136.956829-label_vertebrae-epldo_nk)...
Copying input data to tmp folder...
Straighten spinal cord...
Create temporary folder (/tmp/sct-20190911102137.936778-straighten_spinalcord-vv7u8gdj)...
Copy files to tmp folder...
Window length needs to be >= 3. Returning input signal.
Window length needs to be >= 3. Returning input signal.
Fitting centerline using B-spline approximation
Error on approximation = 9.64 mm
Error on approximation = 5.07 mm
Error on approximation = 2.56 mm
Error on approximation = 0.72 mm
Error on approximation = 0.53 mm
Error on approximation = 0.38 mm
Error on approximation = 0.25 mm
Error on approximation = 0.18 mm
Error on approximation = 0.13 mm
Error on approximation = 0.12 mm
Error on approximation = 0.12 mm
Error on approximation = 0.12 mm
Error on approximation = 0.13 mm
Error on approximation = 0.15 mm
Error on approximation = 0.16 mm
Error on approximation = 0.18 mm
Error on approximation = 0.18 mm
Error on approximation = 0.2 mm
Error on approximation = 0.19 mm
Error on approximation = 0.2 mm
Error on approximation = 0.17 mm
Error on approximation = 0.18 mm
Error on approximation = 0.16 mm
Error on approximation = 0.17 mm
Error on approximation = 0.15 mm
Error on approximation = 0.17 mm
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Singular Matrix in NURBS algorithm -> wrong reconstruction
Create the straight space and the safe zone
Length of spinal cord: 168.1520834395413
Size of spinal cord in z direction: 160.20716225354036
Ratio length/size: 1.0495915480571802
Safe zone boundaries (curved space): [-69.61428680259067, 90.59287545094969]
Safe zone boundaries (straight space): [-73.58674739559113, 94.56533604395015]
Pad input volume to account for spinal cord length...
Time to generate centerline: 59.0 ms
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 216/216 [00:12<00:00, 15.66it/s]
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 272/272 [00:54<00:00, 6.46it/s]
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/mnt/workspace/sct_dev/bin/isct_antsApplyTransforms -d 3 -r tmp.centerline_pad_crop.nii.gz -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -n 'BSpline[3]' # in /tmp/sct-20190911102137.936778-straighten_spinalcord-vv7u8gdj
Generate output files...
File created: ./warp_curve2straight.nii.gz
File created: ./warp_straight2curve.nii.gz
cp /tmp/sct-20190911102137.936778-straighten_spinalcord-vv7u8gdj/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
sct_convert -i /tmp/sct-20190911102137.936778-straighten_spinalcord-vv7u8gdj/tmp.anat_rigid_warp.nii.gz -o ./data_straight.nii
File created: ./data_straight.nii
Remove temporary files...
rm -rf /tmp/sct-20190911102137.936778-straighten_spinalcord-vv7u8gdj
Finished! Elapsed time: 128 s
Resample to 0.5mm isotropic...
sct_resample -i data_straight.nii -mm 0.5x0.5x0.5 -x linear -o data_straightr.nii # in /tmp/sct-20190911102136.956829-label_vertebrae-epldo_nk
Apply straightening to segmentation...
/mnt/workspace/sct_dev/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -r data_straightr.nii -t warp_curve2straight.nii.gz -o segmentation_straight.nii -n Linear # in /tmp/sct-20190911102136.956829-label_vertebrae-epldo_nk
sct_maths -i segmentation_straight.nii -thr 0.5 -o segmentation_straight.nii # in /tmp/sct-20190911102136.956829-label_vertebrae-epldo_nk
Create label to identify disc...
Creating temporary folder...
Run C2-C3 detector...
C2-C3 detected...
Remove temporary files...
rm -rf /tmp/sct-20190911102355.980419-62txwmhp
WARNING: File /tmp/sct-20190911102136.956829-label_vertebrae-epldo_nk/labelz.nii.gz already exists. Will overwrite it.
And apply straightening to label...
/mnt/workspace/sct_dev/bin/isct_antsApplyTransforms -d 3 -i labelz.nii.gz -r data_straightr.nii -t warp_curve2straight.nii.gz -o labelz_straight.nii.gz -n NearestNeighbor # in /tmp/sct-20190911102136.956829-label_vertebrae-epldo_nk
Get z and disc values from straight label...
.. [257, 0]
Look for template...
Path template: /mnt/workspace/sct_dev/data/PAM50
Open template and vertebral levels...
Disc values from template: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
Z-values for each disc: [962, 939, 908, 871, 834, 801, 770, 736, 693, 647, 601, 552, 501, 450, 397, 343, 290, 232, 169, 106, 56]
Distances between discs (in voxel): [23.0, 31.0, 37.0, 37.0, 33.0, 31.0, 34.0, 43.0, 46.0, 46.0, 49.0, 51.0, 51.0, 53.0, 54.0, 53.0, 58.0, 63.0, 63.0, 50.0]
Detect intervertebral discs...
Current disc: 0 (z=257). Direction: superior
.. Peak found: z=9 (correlation = 0.2887059228787826)
Traceback (most recent call last):
File "/mnt/workspace/sct_dev/spinalcordtoolbox/vertebrae/core.py", line 200, in vertebral_detection
approx_distance_to_next_disc = list_distance[list_disc_value_template.index(current_disc - 1)]
ValueError: -1 is not in list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/mnt/workspace/sct_dev/scripts/sct_label_vertebrae.py", line 427, in <module>
main()
File "/mnt/workspace/sct_dev/scripts/sct_label_vertebrae.py", line 372, in main
verbose=verbose, path_template=path_template, path_output=path_output, scale_dist=scale_dist)
File "/mnt/workspace/sct_dev/spinalcordtoolbox/vertebrae/core.py", line 202, in vertebral_detection
sct.printv('WARNING: Disc value not included in template. Using previously-calculated distance: ' + str(approx_distance_to_next_disc))
UnboundLocalError: local variable 'approx_distance_to_next_disc' referenced before assignment
```

advice?

thanks!