Thank you Murat! It started running and eventually failed with this error: Traceback (most recent call last):
File “C:/Users/Bowling Lab/AppData/Local/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/MEMOS/lib/Slicer-5.8/qt-scripted-modules/MEMOS.py”, line 306, in onApplySingleButton
labelFilePath = self.launchInference(volumeNode)
File “C:/Users/Bowling Lab/AppData/Local/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/MEMOS/lib/Slicer-5.8/qt-scripted-modules/MEMOS.py”, line 368, in launchInference
logic.processInference(tempVolumeFile, self.modelPathSingle.currentPath, outputLabelPath, self.colorNode)
File “C:/Users/Bowling Lab/AppData/Local/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/MEMOS/lib/Slicer-5.8/qt-scripted-modules/MEMOS.py”, line 491, in processInference
slicer.util.logProcessOutput(proc)
File “C:\Users\Bowling Lab\AppData\Local\slicer.org\Slicer 5.8.1\bin\Python\slicer\util.py”, line 3862, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[‘C:/Users/Bowling Lab/AppData/Local/slicer.org/Slicer 5.8.1/bin/../bin\\PythonSlicer.EXE’, ‘C:/Users/Bowling Lab/AppData/Local/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/MEMOS/lib/Slicer-5.8/qt-scripted-modules\\Scripts\\MEMOS_inference.py’, ‘–volume-path’, “{‘image’: ‘C:/Users/Bowling Lab/AppData/Local/Temp/Slicer\\\\tempMEMOSVolume\\\\2793: Linear Attenuation [1-cm] (2793).nii.gz’}”, ‘–model-path’, ‘C:/Users/Bowling Lab/AppData/Local/slicer.org/Slicer/cache/SlicerIO\\best_metric_model_largePatch_noise.pth’, ‘–output-path’, ‘C:/Users/Bowling Lab/AppData/Local/Temp/Slicer\\tempMEMOSOut\\2793: Linear Attenuation [1-cm] (2793)_seg.nii.gz’, ‘–color-node’, ‘vtkMRMLColorTableNode (000001EA9A67B360)\n ID: vtkMRMLColorTableNode1\n ClassName: vtkMRMLColorTableNode\n Name: KOMP2\n Debug: false\n MTime: 261593\n Description: A color table read in from a text file, each line of the format: IntegerLabel Name R G B Alpha\n SingletonTag: (none)\n HideFromEditors: false\n Selectable: true\n Selected: false\n UndoEnabled: false\n Attributes:\n Category:File\n Node references:\n storage [storageNodeRef]: vtkMRMLColorTableStorageNode22\n StorageNodeIDs[0]: vtkMRMLColorTableStorageNode22\n Name: KOMP2\n Type: (File)\n NoName = (none)\n Names array initialised: true\n Color Names:\n 0 background (0, 0, 0, 1)\n 1 left lung (0.772549, 0.647059, 0.568627, 1)\n 2 cranial lobe (0.501961, 0.682353, 0.501961, 1)\n 3 middle lobe (0.945098, 0.839216, 0.568627, 1)\n 4 caudal lobe (0.694118, 0.478431, 0.396078, 1)\n 5 accessory lobe (0.435294, 0.721569, 0.823529, 1)\n 6 left kidney (0.72549, 0.4, 0.32549, 1)\n 7 right kidney (0.72549, 0.4, 0.32549, 1)\n 8 stomach wall (0.847059, 0.396078, 0.309804, 1)\n 9 stomach lumen (0.866667, 0.509804, 0.396078, 1)\n 10 medial lobe of liver (0.564706, 0.933333, 0.564706, 1)\n …\n Look up table:\n Debug: Off\n Modified Time: 261572\n Reference Count: 1\n Registered Events: \n Registered Observers:\n vtkObserver (000001EA9C545DA0)\n Event: 33\n EventName: ModifiedEvent\n Command: 000001EA99D315A0\n Priority: 0\n Tag: 2\n vtkObserver (000001EA9C545D70)\n Event: 2\n EventName: DeleteEvent\n Command: 000001EA99D315A0\n Priority: 0\n Tag: 1\n Alpha: 1\n VectorMode: Component\n VectorComponent: 0\n VectorSize: -1\n IndexedLookup: OFF\n AnnotatedValues: 0 entries.\n TableRange: (0, 50)\n Scale: Linear\n HueRange: (0, 0.66667)\n SaturationRange: (1, 1)\n ValueRange: (1, 1)\n AlphaRange: (1, 1)\n NanColor: (0.5, 0, 0, 1)\n BelowRangeColor: (0, 0, 0, 1)\n UseBelowRangeColor: OFF\n AboveRangeColor: (1, 1, 1, 1)\n UseAboveRangeColor: OFF\n NumberOfTableValues: 51\n NumberOfColors: 51\n Ramp: SCurve\n InsertTime: 261571\n BuildTime: 0\n Table: \n Debug: Off\n Modified Time: 261316\n Reference Count: 1\n Registered Events: (none)\n Name: (none)\n Data type: unsigned char\n Size: 1040\n MaxId: 203\n NumberOfComponents: 4\n Information: 0000000000000000\n Name: (none)\n Number Of Components: 4\n Number Of Tuples: 51\n Size: 1040\n MaxId: 203\n LookupTable: (none)\n\n’]’ returned non-zero exit status 1. The data I am trying to analyse is not very good (very noisy), would that be the reason for failure?
