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lassoan / SlicerMONAIAuto3DSeg

Extension for 3D Slicer for running MONAI Auto3DSeg models
MIT License
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run testData branch MONAIAuto3DSegTest error #79

Closed zist8888 closed 2 months ago

zist8888 commented 2 months ago

Dependencies are set up successfully. Processing started Writing input file to /tmp/Slicer-ubuntu/SlicerTemp2024-09-26_16+31+46.165/input-volume.nrrd Creating segmentations with MONAIAuto3DSeg AI... Auto3DSeg command: ['/data/soft/Slicer-5.7.0-2024-03-25-linux-amd64/bin/../bin/PythonSlicer', '/data/soft/Slicer-5.7.0-2024-03-25-linux-amd64/sl icer.org/Extensions-32785/MONAIAuto3DSeg/lib/Slicer-5.7/qt-scripted-modules/Scripts/auto3dseg_segresnet_inference.py', '--model-file', '/home/ub untu/.MONAIAuto3DSeg/models/abdominal-organs-3mm/model.pt', '--image-file', '/tmp/Slicer-ubuntu/SlicerTemp2024-09-26_16+31+46.165/input-volu me.nrrd', '--result-file', '/data/soft/Slicer-5.7.0-2024-03-25-linux-amd64/output-segmentation.nii.gz'] apex.normalization.InstanceNorm3dNVFuser is not installed properly, use nn.InstanceNorm3d instead. Model epoch 294 metric 0.9070999026298523 Using crop_foreground Using resample with resample_resolution [3.0, 3.0, 3.0] Running Inference ...

0%| | 0/6 [00:00<?, ?it/s]Applied workaround for CuDNN issue, install nvrtc.so (Triggered internally at ../aten/src/ATen/native/cudnn /Conv_v8.cpp:84.)

17%|█▋ | 1/6 [00:00<00:01, 3.50it100%|██████████| 6/6 [00:0100%|██████████| 6/6 [00:0Logits torch.Size([1, 25, 160, 133, 134]) Converting logits into predictions preds torch.Size([1, 1, 160, 133, 134]) preds inverted torch.Size([512, 512, 321]) Computation time log: Loading volumes: 1.35 seconds Preprocessing: 2.60 seconds Inference: 0.53 seconds Logits: 0.33 seconds Preds: 0.15 seconds Convert to array: 0.32 seconds Save: 4.06 seconds ALL DONE, result saved in /data/soft/Slicer-5.7.0-2024-03-25-linux-amd64/output-segmentation.nii.gz Processing failed with return code 1002 Cleaning up temporary folder. Processing failed after 16.58 seconds. double free or corruption (!prev) error: [/data/soft/Slicer-5.7.0-2024-03-25-linux-amd64/bin/SlicerApp-real] exit abnormally - Report the problem.

run Test without slicer3D UI，I get error，save file cannt open ，why？tks

lassoan commented 2 months ago

Phrase user the latest Slicer Stable Release or latest Slicer Preview Release and key is know if you run into any issues.

lassoan commented 2 months ago

The problem is that the result file format is incorrect (you get .nii.gz, while .nrrd file format should be used instead).

zist8888 commented 2 months ago

you are right,i have modified at the afternoon,thanks for replying!