Trying to track down the problem. sct_label_vertebrae references sct_straighten_spinalcord, which references sct_concat_transfo, which is approximately where the error was generated in sct_straighten_spinalcord just by looking at the printed statements. Last few lines of output preceeding error as follows:

*Estimate b-spline transformation: curve --> straight...
isctANTSLandmarksBSplineTransform tmp.landmarksstraight.nii.gz tmp.landmarkscurved.nii.gz tmp.curve2straightrigid.txt tmp.warpcurve2straight.nii.gz 3x3x5 3 LandmarksRealCurve.txt LandmarksRealStraight.txt 3 0
crop
isctcropimage -i tmp.landmarksstraight.nii.gz -o tmp.landmarksstraightcrop.nii.gz -dim 0,1,2 -bmax
Cropping the following region:
Dimension 0: 159 221
Dimension 1: 159 221
Dimension 2: 29 81

Done! To view results, type:
fslview tmp.landmarksstraightcrop.nii.gz &

Concatenate rigid and non-linear transformations...
sctconcattransfo -w tmp.curve2straightrigid.txt,tmp.warpcurve2straight.nii.gz -d tmp.landmarksstraightcrop.nii.gz -o tmp.curve2straight.nii.gz

ERROR: The file tmp.curve2straightrigid.txt does not exist. Exit program.

*

sct_testing ran without errors excepting a fail on sct_get_centerline. Propseg and process_segmentation worked well, but this error is identical whether using output from propseg or process_segmentation as an input.

Any help is appreciated.

Thanks