Hi,
Running the labelling step and shape-based analysis, the qc report (html file) does not seem to update. I still have only the line corresponding to the segmentation.
Please see below for the full log. Thank you for the help,
Best,
Nabila
sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc /Users/fwlab_nb/qc_singleSubj
--
Creating temporary folder (/var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-44_label-vertebrae_oy2fmpws)
Copying input data to tmp folder...
Straighten spinal cord...
**Reusing existing warping field which seems to be valid**
cp /Users/fwlab_nb/sct_course_data/single_subject/data/t2/straightening.cache straightening.cache
cp /Users/fwlab_nb/sct_course_data/single_subject/data/t2/warp_curve2straight.nii.gz warp_curve2straight.nii.gz
cp /Users/fwlab_nb/sct_course_data/single_subject/data/t2/warp_straight2curve.nii.gz warp_straight2curve.nii.gz
cp /Users/fwlab_nb/sct_course_data/single_subject/data/t2/straight_ref.nii.gz straight_ref.nii.gz
Resample to 0.5mm isotropic...
load data...
Apply straightening to segmentation...
File /private/var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-44_label-vertebrae_oy2fmpws/segmentation_straight.nii already exists. Will overwrite it.
Create label to identify disc...
Creating temporary folder...
Creating temporary folder (/var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-47_detect-c2c3_9emqvo0n)
Image header specifies datatype 'float32', but array is of type 'int16'. Header metadata will be overwritten to use 'int16'.
Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'.
Run C2-C3 detector...
Image header specifies datatype 'float32', but array is of type 'uint8'. Header metadata will be overwritten to use 'uint8'.
C2-C3 detected...
Remove temporary files...
rm -rf /var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-47_detect-c2c3_9emqvo0n
File /var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-44_label-vertebrae_oy2fmpws/labelz.nii.gz already exists. Will overwrite it.
And apply straightening to label...
Get z and disc values from straight label...
.. [308, 3]
Look for template...
Path template: /Users/fwlab_nb/sct_6.5/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: [984, 938, 907, 870, 833, 800, 769, 735, 692, 646, 600, 551, 500, 449, 396, 342, 289, 231, 168, 105, 39]
Distances between discs (in voxel): [46.0, 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, 66.0]
Detect intervertebral discs...
Current disc: 2 (z=308). Direction: superior
.. Peak found: z=-3 (correlation = 0.5731065903895622)
Current disc: 1 (z=336). Direction: superior
.. correcting factor: 1.0
.. Switching to inferior direction.
Current disc: 3 (z=271). Direction: inferior
.. Peak found: z=-1 (correlation = 0.4609616422279576)
.. correcting factor: 0.972972972972973
Current disc: 4 (z=234). Direction: inferior
.. Peak found: z=-1 (correlation = 0.49005321018819764)
.. correcting factor: 0.981981981981982
Current disc: 5 (z=201). Direction: inferior
.. Peak found: z=-2 (correlation = 0.5298939824797383)
.. correcting factor: 0.9940622440622441
Current disc: 6 (z=168). Direction: inferior
.. Peak found: z=0 (correlation = 0.6480323638269871)
.. correcting factor: 0.9952497952497954
Current disc: 7 (z=134). Direction: inferior
.. Peak found: z=3 (correlation = 0.5134397586952049)
.. correcting factor: 0.981335613688555
Current disc: 8 (z=95). Direction: inferior
.. Peak found: z=1 (correlation = 0.5087236005179484)
.. correcting factor: 0.9773574363177647
Current disc: 9 (z=51). Direction: inferior
.. Peak found: z=4 (correlation = 0.4946196737508683)
.. correcting factor: 0.9666008002563049
Current disc: 10 (z=11). Direction: inferior
.. Peak found: z=5 (correlation = 0.4957669456823823)
.. correcting factor: 0.9534036098896623
Adding top disc based on adjusted template distance: #0
.. approximate distance: 44
Un-straighten labeling...
Cleaning labeled segmentation:
removing labeled voxels outside segmentation...
Done cleaning.
File /private/var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-44_label-vertebrae_oy2fmpws/segmentation_labeled.nii already exists. Will overwrite it.
Label discs...
Un-straighten labeled discs...
Creating temporary folder (/var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-51_apply-transfo-3d-label_26z_3u4q)
File segmentation_labeled_disc.nii already exists. Will overwrite it.
Generate output files...
File /Users/fwlab_nb/sct_course_data/single_subject/data/t2/t2_seg_labeled.nii.gz already exists. Deleting it..
File created: /Users/fwlab_nb/sct_course_data/single_subject/data/t2/t2_seg_labeled.nii.gz
File /Users/fwlab_nb/sct_course_data/single_subject/data/t2/t2_seg_labeled_discs.nii.gz already exists. Deleting it..
File created: /Users/fwlab_nb/sct_course_data/single_subject/data/t2/t2_seg_labeled_discs.nii.gz
File /Users/fwlab_nb/sct_course_data/single_subject/data/t2/straightening.cache already exists. Deleting it..
mv /var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-44_label-vertebrae_oy2fmpws/straightening.cache /Users/fwlab_nb/sct_course_data/single_subject/data/t2/straightening.cache
File created: /Users/fwlab_nb/sct_course_data/single_subject/data/t2/straightening.cache
File /Users/fwlab_nb/sct_course_data/single_subject/data/t2/warp_curve2straight.nii.gz already exists. Deleting it..
mv /var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-44_label-vertebrae_oy2fmpws/warp_curve2straight.nii.gz /Users/fwlab_nb/sct_course_data/single_subject/data/t2/warp_curve2straight.nii.gz
File created: /Users/fwlab_nb/sct_course_data/single_subject/data/t2/warp_curve2straight.nii.gz
File /Users/fwlab_nb/sct_course_data/single_subject/data/t2/warp_straight2curve.nii.gz already exists. Deleting it..
mv /var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-44_label-vertebrae_oy2fmpws/warp_straight2curve.nii.gz /Users/fwlab_nb/sct_course_data/single_subject/data/t2/warp_straight2curve.nii.gz
File created: /Users/fwlab_nb/sct_course_data/single_subject/data/t2/warp_straight2curve.nii.gz
File /Users/fwlab_nb/sct_course_data/single_subject/data/t2/straight_ref.nii.gz already exists. Deleting it..
mv /var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-44_label-vertebrae_oy2fmpws/straight_ref.nii.gz /Users/fwlab_nb/sct_course_data/single_subject/data/t2/straight_ref.nii.gz
File created: /Users/fwlab_nb/sct_course_data/single_subject/data/t2/straight_ref.nii.gz
Remove temporary files...
rm -rf /var/folders/bb/tkk0kp15763g75kpdjyr_rg40000gn/T/sct_2024-12-09_17-00-44_label-vertebrae_oy2fmpws
*** Generating Quality Control (QC) html report ***
/Users/fwlab_nb/qc_singleSubj/single_subject/data/t2/sct_label_vertebrae/2024_12_09_170053.824301/background_img.png
Traceback (most recent call last):
File "/Users/fwlab_nb/sct_6.5/spinalcordtoolbox/scripts/sct_label_vertebrae.py", line 507, in <module>
main(sys.argv[1:])
File "/Users/fwlab_nb/sct_6.5/spinalcordtoolbox/scripts/sct_label_vertebrae.py", line 498, in main
generate_qc(fname_in, fname_seg=labeled_seg_file, args=argv, path_qc=os.path.abspath(path_qc),
File "/Users/fwlab_nb/sct_6.5/spinalcordtoolbox/reports/qc.py", line 632, in generate_qc
qc_image._make_QC_image_for_3d_volumes(img, mask, plane, imgs_to_generate)
File "/Users/fwlab_nb/sct_6.5/python/envs/venv_sct/lib/python3.9/contextlib.py", line 126, in __exit__
next(self.gen)
File "/Users/fwlab_nb/sct_6.5/spinalcordtoolbox/reports/qc2.py", line 130, in create_qc_entry
path_index_html = refresh_qc_entries.main(path_qc)
File "/Users/fwlab_nb/sct_6.5/spinalcordtoolbox/reports/assets/_assets/py/refresh_qc_entries.py", line 42, in main
json_data.append(json.load(file))
File "/Users/fwlab_nb/sct_6.5/python/envs/venv_sct/lib/python3.9/json/__init__.py", line 293, in load
return loads(fp.read(),
File "/Users/fwlab_nb/sct_6.5/python/envs/venv_sct/lib/python3.9/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/Users/fwlab_nb/sct_6.5/python/envs/venv_sct/lib/python3.9/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/Users/fwlab_nb/sct_6.5/python/envs/venv_sct/lib/python3.9/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 2 column 1 (char 1)
fwlab_nb@Mac t2 % sct_process_segmentation -i t2_seg.nii.gz -vert 3:4 -vertfile t2_seg_labeled.nii.gz
-o csa_c3c4.csv
