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`dcm-brno_2024-07-14` processing errors #17

Open valosekj opened 1 month ago

valosekj commented 1 month ago

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 ```bash $ 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 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 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 commented 1 month ago
`sub-3758B6378B_ses-6378B_acq-ZOOMit_dir-AP_dwi.nii.gz` is unusable: image image
`sub-3998B6406B_ses-6406B_acq-ZOOMit_dir-AP_dwi.nii.gz` is unusable: image image

--> adding both to exclude.yml in https://github.com/valosekj/dcm-brno/commit/1a8fee4bc9a8347ee9b5692507b8dd2aa025e598

valosekj commented 1 month ago

QC: