dcm-brno_2024-07-14 processing errors

[valosekj]

dcm-brno_2024-07-14 -- subjects with surgery (https://github.com/valosekj/dcm-brno/blob/main/surgery.yml)

Error logs for two subjects:

$ dcm-brno_2024-07-14/log$ ls -1 err*
err.02_process_data_sub-3758B6378B_ses-6378B.log
err.02_process_data_sub-3998B6406B_ses-6406B.log

details

$ dcm-brno_2024-07-14/log$ for err in err*;do echo $err; tail -30 $err; echo "";done
err.02_process_data_sub-3758B6378B_ses-6378B.log

itksnap -g sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco_dwi_mean.nii.gz -o label_sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_t2.nii.gz label_sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_gm.nii.gz label_sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_wm.nii.gz

+ sct_qc -i sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco_dwi_mean.nii.gz -s label_sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_levels.nii.gz -p sct_label_vertebrae -qc /md1/valosek/results/dcm-brno_2024-07-14/qc -qc-subject sub-3758B6378B/ses-6378B

--
Spinal Cord Toolbox (git-master-65e44b5068fe5d8a094e3e0571566c01d2d460ab)

sct_qc -i sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco_dwi_mean.nii.gz -s label_sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_levels.nii.gz -p sct_label_vertebrae -qc /md1/valosek/results/dcm-brno_2024-07-14/qc -qc-subject sub-3758B6378B/ses-6378B
--


*** Generate Quality Control (QC) html report ***
QcImage: layout with Sagittal slice
Traceback (most recent call last):
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/scripts/sct_qc.py", line 122, in <module>
    main(sys.argv[1:])
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/scripts/sct_qc.py", line 105, in main
    generate_qc(fname_in1=arguments.i,
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/qc.py", line 773, in generate_qc
    QcImage(
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/qc.py", line 295, in layout
    img, *mask = qcslice_layout(qcslice)
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/qc.py", line 708, in qcslice_layout
    def qcslice_layout(x): return x.single()
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/slice.py", line 241, in single
    index = self.get_center_spit()
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/slice.py", line 424, in get_center_spit
    raise ValueError("Label/segmentation image is empty. Can't retrieve RL slice indices.")
ValueError: Label/segmentation image is empty. Can't retrieve RL slice indices.

err.02_process_data_sub-3998B6406B_ses-6406B.log

itksnap -g sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco_dwi_mean.nii.gz -o label_sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_t2.nii.gz label_sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_gm.nii.gz label_sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_wm.nii.gz

+ sct_qc -i sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco_dwi_mean.nii.gz -s label_sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_levels.nii.gz -p sct_label_vertebrae -qc /md1/valosek/results/dcm-brno_2024-07-14/qc -qc-subject sub-3998B6406B/ses-6406B

--
Spinal Cord Toolbox (git-master-65e44b5068fe5d8a094e3e0571566c01d2d460ab)

sct_qc -i sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco_dwi_mean.nii.gz -s label_sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi_crop_crop_moco/template/PAM50_levels.nii.gz -p sct_label_vertebrae -qc /md1/valosek/results/dcm-brno_2024-07-14/qc -qc-subject sub-3998B6406B/ses-6406B
--


*** Generate Quality Control (QC) html report ***
QcImage: layout with Sagittal slice
Traceback (most recent call last):
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/scripts/sct_qc.py", line 122, in <module>
    main(sys.argv[1:])
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/scripts/sct_qc.py", line 105, in main
    generate_qc(fname_in1=arguments.i,
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/qc.py", line 773, in generate_qc
    QcImage(
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/qc.py", line 295, in layout
    img, *mask = qcslice_layout(qcslice)
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/qc.py", line 708, in qcslice_layout
    def qcslice_layout(x): return x.single()
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/slice.py", line 241, in single
    index = self.get_center_spit()
  File "/home/valosek/code/sct_v6.3/spinalcordtoolbox/reports/slice.py", line 424, in get_center_spit
    raise ValueError("Label/segmentation image is empty. Can't retrieve RL slice indices.")
ValueError: Label/segmentation image is empty. Can't retrieve RL slice indices.

[valosekj]

`sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi.nii.gz` is unusable:

`sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi.nii.gz` is unusable:

--> adding both to exclude.yml in 1a8fee4

[valosekj]

QC:

• SC seg (contrast-agnostic model) on crop_crop_moco_dwi_mean.nii.gz - look good for all subjects except for two listed in dcm-brno_2024-07-14 processing errors #17 (comment)
• SC labeling (PAM50_levels.nii.gz in DWI space) on crop_crop_moco_dwi_mean.nii.gz - look good for all subjects expect for two listed in dcm-brno_2024-07-14 processing errors #17 (comment)