Hello @LISA_mri_challenge, I tried to make a submission to Task 2(a). My file seems OK and contains all the predictions in the prescribed format. A few noteworthy lines in the error log were: STDERR: ... AttributeError: `np.Inf` was removed in the NumPy 2.0 release. Use `np.inf` instead. STDERR: ... File "/app/scripts/task2a.py", line 40, in compute_metrics STDERR: ... File "/app/scripts/task2a.py", line 31, in score STDERR: ... File "/usr/local/lib/python3.10/site-packages/surface_distance/metrics.py", line 257, in compute_surface_distances STDERR: ... distmap_gt = np.Inf * np.ones(borders_gt.shape) Can you please confirm that the script to score submissions is using the correct versions of the libraries? Or it is something wrong on my side.

Created by Yasar Mehmood YasarMehmood
Hi @YasarMehmood and @Musti, The scoring step failed because the uploaded .nii files could not be processed correctly, so the required results.json was not generated. This usually indicates an issue with the prediction labels or file format. Please re-check your submitted .nii files and confirm that you are using the correct label values for segmentation: 0 (Background): Areas that do not belong to any segmentation. 1 (Left Hippocampus): Identifies the left hippocampus in the segmentation maps. 2 (Right Hippocampus): Identifies the right hippocampus in the segmentation maps. If your predictions use labels outside of this definition, or if the files are not valid NIfTI volumes with the expected dimensions and orientation, the evaluation will fail. Please verify your outputs and re-submit corrected files so the scoring system can proceed. Thanks, The LISA 2025 Challenge Organizers
Hello @LISA_mri_challenge, I am writing to follow up on the issue. Please let us know once the issue is resolved. Best, Yasar Mehmood
Hello, We will correct this issue ASAP. Thank you for bringing it to our attention. Best, The LISA 2025 Challenge Organizers
Hi @LISA_mri_challenge! I'm also getting this error when I wanted to submit my results: AttributeError: `np.Inf` was removed in the NumPy 2.0 release. Use `np.inf` instead. STDERR: 2025-08-18T12:47:46.126674800Z [job score.cwl] Max memory used: 76MiB STDERR: 2025-08-18T12:47:46.126676028Z INFO:cwltool:[job score.cwl] Max memory used: 76MiB STDERR: 2025-08-18T12:47:46.126677204Z [job score.cwl] Job error: STDERR: 2025-08-18T12:47:46.126678377Z ("Error collecting output for parameter 'results':\nLISA_infra-main/wf-Task2a/steps/score.cwl:41:5: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2025-08-18T12:47:46.126679793Z ERROR:cwltool:[job score.cwl] Job error: STDERR: 2025-08-18T12:47:46.126681019Z ("Error collecting output for parameter 'results':\nLISA_infra-main/wf-Task2a/steps/score.cwl:41:5: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2025-08-18T12:47:46.126682466Z [job score.cwl] completed permanentFail STDERR: 2025-08-18T12:47:46.126683702Z WARNING:cwltool:[job score.cwl] completed permanentFail STDERR: 2025-08-18T12:47:46.126684889Z Traceback (most recent call last): STDERR: 2025-08-18T12:47:46.126686065Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2025-08-18T12:47:46.126687335Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2025-08-18T12:47:46.126688547Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner STDERR: 2025-08-18T12:47:46.126689781Z returnValues = self._run(jobGraph, fileStore) STDERR: 2025-08-18T12:47:46.126690957Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run STDERR: 2025-08-18T12:47:46.126692243Z return self.run(fileStore) STDERR: 2025-08-18T12:47:46.126693439Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2025-08-18T12:47:46.126696464Z raise cwltool.errors.WorkflowException(status) STDERR: 2025-08-18T12:47:46.126697746Z cwltool.errors.WorkflowException: permanentFail STDERR: 2025-08-18T12:47:46.126698910Z ERROR:toil.worker:Exiting the worker because of a failed job on host 04155a8fbf87 STDERR: 2025-08-18T12:47:46.126700185Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/84130d40-fb13-4aa5-acdd-4a4da8c5adab/LISA_infra-main/wf-Task2a/steps/score.cwl' user passed empty string for name kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_84130d40-fb13-4aa5-acdd-4a4da8c5adab_LISA_infra-main_wf-Task2a_steps_score.cwl/instance-9ytec3at with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_84130d40-fb13-4aa5-acdd-4a4da8c5adab_LISA_infra-main_wf-Task2a_steps_score.cwl/instance-9ytec3at to 0 STDERR: 2025-08-18T12:47:46.126702177Z <========= --------------------------------------------------------- Hope that you guys can help us solve this issue and identify if it is being caused from our or your side :) Best, Musti

Scoring Error on Latest Submission (Task 2a) - NumPy Related page is loading…