Closed grinerD closed 9 months ago
I received a license for the vertebrae_body segmentations, but when I try running it I get the following error:
Predicting s01: perform_everything_on_gpu: True 100%|██████████| 18/18 [00:00<00:00, 185.41it/s] Prediction done, transferring to CPU if needed sending off prediction to background worker for resampling and export done with s01 Predicted in 7.23s Resampling... back to original shape: (512, 512, 467) Undoing canonical... --------------------------------------------------------------------------- KeyError Traceback (most recent call last) Cell In[10], line 28 24 print('\nSaving to: {}'.format(segmentations_directories[directory] + '/spine.nii.gz\n')) 26 torch.cuda.empty_cache() ---> 28 totalsegmentator(dicom_directories[directory], segmentations_directories[directory] + '/vert_body.nii.gz', 29 ml=True, 30 roi_subset=rois_vert_body, 31 #statistics=True, 32 #device="cpu", 33 verbose=True) 35 print('\nSaving to: {}'.format(segmentations_directories[directory] + '/vert_body.nii.gz\n')) 37 torch.cuda.empty_cache() File /opt/conda/envs/py310/lib/python3.10/site-packages/totalsegmentator/python_api.py:272, in totalsegmentator(input, output, ml, nr_thr_resamp, nr_thr_saving, fast, nora_tag, preview, task, roi_subset, statistics, radiomics, crop_path, body_seg, force_split, output_type, quiet, verbose, test, skip_saving, device, license_number, statistics_exclude_masks_at_border, no_derived_masks, v1_order) 270 roi_subset_crop = crop if crop is not None else roi_subset 271 for roi in roi_subset_crop: --> 272 crop_mask[organ_seg_data == class_map_inv[roi]] = 1 273 crop_mask = nib.Nifti1Image(crop_mask, organ_seg.affine) 274 crop_addon = [20,20,20] KeyError: 'vertebrae_body'
Sorry, I just realized I need to use task and not roi_subset.
I received a license for the vertebrae_body segmentations, but when I try running it I get the following error: