Hi SCT team,
We were thinking of looking at some spinal cord area measurements in our subjects - we’ve gone through the usual steps, but appear to be missing something:
sct_process_segmentation -i sanlm_structural_seg.nii.gz -p csa -vert 3:9 -perlevel 1 -o csa_perlevel.csv
Compute CSA... WARNING: Your segmentation does not seem continuous, which could cause wrong estimations at the problematic slices. Please check it, especially at the extremities. Remove temporary files... rm -rf /var/folders/y_/1ktpkszd3qqdqf18pv7qsrkh0000gn/T/sct-20190312195700.531761-p3TWJZ Traceback (most recent call last): File "/Users/jon/sct_4.0.0-beta.1/scripts/sct_process_segmentation.py", line 256, in <module> main(sys.argv[1:]) File "/Users/jon/sct_4.0.0-beta.1/scripts/sct_process_segmentation.py", line 223, in main group_funcs=group_funcs) File "/Users/jon/sct_4.0.0-beta.1/spinalcordtoolbox/aggregate_slicewise.py", line 79, in aggregate_per_slice_or_level im_vert_level = Image(vert_level).change_orientation('RPI') File "/Users/jon/sct_4.0.0-beta.1/spinalcordtoolbox/image.py", line 235, in __init__ self.loadFromPath(param, verbose) File "/Users/jon/sct_4.0.0-beta.1/spinalcordtoolbox/image.py", line 318, in loadFromPath self.im_file = nibabel.load(path) File "/Users/jon/sct_4.0.0-beta.1/python/lib/python2.7/site-packages/nibabel/loadsave.py", line 40, in load raise FileNotFoundError("No such file: '%s'" % filename) nibabel.py3k.FileNotFoundError: No such file: './label/template/PAM50_levels.nii.gz' Sentry is attempting to send 1 pending error messages Waiting up to 10 seconds Press Ctrl-C to quit Total processing time: 0 min 4 s
Should the missing file ‘./label/template/PAM50_levels.nii.gz’ be generated automatically by sct_register_to_template or do we need to create it manually? I guess that pointing -vertfile to the PAM50_levels.nii.gz in $SCT_DIR/data/PAM50/template/ would be the wrong thing as it hasn’t been transformed into the space of the subject?
Any pointers to what I’m doing wrong?