Runtime error on mac #8
Description
I tried the extension with yesterday's nightly, and got the following error.
Full log:
[95m**************************************************************[0m
[95m** CITATION NOTICE **[0m
[95m** -------------------------------------------------------- **[0m
[95m** [0m [95m **[0m
[95m** [0mYou are running an MHub model. Cite the MHub platform in[95m **[0m
[95m** [0m your work. Visit https://mhub.ai/cite for more. [95m **[0m
[95m** [0m [95m **[0m
[95m** [0mYou are running a model. Please cite the authors of the [95m **[0m
[95m** [0mmodel and the MHub model url in your work: [95m **[0m
[95m** [0m The model card and run instructions for this model are [95m **[0m
[95m** [0m publicly available on the MHub platform under https://m/[95m **[0m
[95m** [0m hub.ai/models/totalsegmentator. [95m **[0m
[95m** [0m [95m **[0m
[95m** [0mThank you for using MHub! [95m **[0m
[95m** [0m [95m **[0m
[95m**************************************************************[0m
[95m**************************************************************[0m
[95m** CITATION NOTICE **[0m
[95m** -------------------------------------------------------- **[0m
[95m** [0m [95m **[0m
[95m** [0mYou are running an MHub model. Cite the MHub platform in[95m **[0m
[95m** [0m your work. Visit https://mhub.ai/cite for more. [95m **[0m
[95m** [0m [95m **[0m
[95m** [0mYou are running a model. Please cite the authors of the [95m **[0m
[95m** [0mmodel and the MHub model url in your work: [95m **[0m
[95m** [0m The model card and run instructions for this model are [95m **[0m
[95m** [0m publicly available on the MHub platform under https://m/[95m **[0m
[95m** [0m hub.ai/models/totalsegmentator. [95m **[0m
[95m** [0m [95m **[0m
[95m** [0mThank you for using MHub! [95m **[0m
[95m** [0m [95m **[0m
[95m**************************************************************[0m
--------------------------
Start DicomImporter
> source input dir: input_data --> /app/data/input_data
> import sort dir: sorted_data --> /app/data/sorted_data
sorting dicom data
> input dir: /app/data/input_data
> output dir: /app/data/sorted_data
> schema: %SeriesInstanceUID/dicom/%SOPInstanceUID.dcm
> creating output folder: /app/data/sorted_data
>> run: dicomsort -k -u /app/data/input_data /app/data/sorted_data/%SeriesInstanceUID/dicom/%SOPInstanceUID.dcm
0%| | 0/162 [00:00<?, ?it/s]
5%|▍ | 8/162 [00:00<00:02, 73.93it/s]
10%|▉ | 16/162 [00:00<00:01, 74.34it/s]
15%|█▍ | 24/162 [00:00<00:01, 73.36it/s]
20%|██ | 33/162 [00:00<00:01, 75.16it/s]
25%|██▌ | 41/162 [00:00<00:01, 75.68it/s]
31%|███ | 50/162 [00:00<00:01, 78.64it/s]
36%|███▋ | 59/162 [00:00<00:01, 79.89it/s]
42%|████▏ | 68/162 [00:00<00:01, 80.41it/s]
48%|████▊ | 77/162 [00:00<00:01, 81.73it/s]
53%|█████▎ | 86/162 [00:01<00:00, 79.26it/s]
59%|█████▊ | 95/162 [00:01<00:00, 80.38it/s]
65%|██████▍ | 105/162 [00:01<00:00, 83.90it/s]
71%|███████ | 115/162 [00:01<00:00, 87.50it/s]
77%|███████▋ | 125/162 [00:01<00:00, 90.63it/s]
83%|████████▎ | 135/162 [00:01<00:00, 92.32it/s]
90%|████████▉ | 145/162 [00:01<00:00, 93.87it/s]
96%|█████████▌| 155/162 [00:01<00:00, 94.60it/s]
100%|██████████| 162/162 [00:01<00:00, 85.09it/s]
Files sorted
> importing sorted instance (1/1): 1.2.840.113654.2.55.305538394446738410906709753576946604022
> related instances: 0
Done in 3.65486 seconds.
--------------------------
Start NiftiConverter
Running 'plastimatch convert' with the specified arguments:
--input /app/data/sorted_data/1.2.840.113654.2.55.305538394446738410906709753576946604022/dicom
--output-img /app/data/sorted_data/1.2.840.113654.2.55.305538394446738410906709753576946604022/nifti/dicom.nii.gz
... Done.
Done in 26.416 seconds.
--------------------------
Start TotalSegmentatorMLRunner
Generating multi-label output ('--ml')
Running TotalSegmentator in fast mode ('--fast', 3mm)
>> run: TotalSegmentator -i /app/data/sorted_data/1.2.840.113654.2.55.305538394446738410906709753576946604022/nifti/dicom.nii.gz -o /app/data/sorted_data/1.2.840.113654.2.55.305538394446738410906709753576946604022/nifti/segmentations.nii.gz --ml --fast
Docker image details.
Of note, Docker is rather old at v4.18.0. I am going to upgrade it now and retry.