Operating system and version
Ubuntu 22.04
CPU architecture
x86_64 (PC, Intel Mac, other Intel/AMD)
ANTs code version
2.5.2
ANTs installation type
Downloaded Github release binaries
Summary of the problem
Getting the following error when running a 3 class tissue segmentation of the hippocampus/amygdala.
Progress:
WARNING: In /home/runner/work/ANTs/ANTs/ImageSegmentation/antsHistogramParzenWindowsListSampleFunction.hxx, line 57
HistogramParzenWindowsListSampleFunction (0x55a3c60883d0): The input list sample has <= 1 element.Function evaluations will be equal to 0.
Iteration 0 (of 5): posterior probability = 0 (annealing temperature = 1)
itk::ExceptionObject (0x55a3c60b8cf0)
Location: "unknown"
File: /home/runner/work/_temp/build/staging/include/ITK-5.4/itkLabelMap.hxx
Line: 180
Description: ITK ERROR: LabelMap(0x55a3c6f42450): Can't access label object at position 2. The label map has only 2 label objects registered
Seems to work with v2.3.5.post76-g28dd25c
Note if I change the number of classes to 2, without changing any other input the command works
Commands to reproduce the problem.
Atropos -a 122317_b0b1000_MD_plusFA.nii.gz -x 122317_initialization_LEFT_HIPPOAMYG.nii.gz -i PriorProbabilityImages[3,122317_initialization_INITAMYGHIPPO_LH_%02d.nii.gz,0.3,0.0001] -m [0.3, 2x2x2] --use-partial-volume-likelihoods false -s 1x3 -s 1x2 -o [122317_initialization_INITAMYGHIPPO_LH_LABELS.nii.gz, 122317_initialization_INITAMYGHIPPO_LH_PROBS_%02d.nii.gz] -k HistogramParzenWindows[1.0,32] -v 1
Output of the command with verbose output.
"""Atropos -a 122317_b0b1000_MD_plusFA.nii.gz -x 122317_initialization_LEFT_HIPPOAMYG.nii.gz -i PriorProbabilityImages[3,122317_initialization_INITAMYGHIPPO_LH_%02d.nii.gz,0.3,0.0001] -m [0.3, 2x2x2] --use-partial-volume-likelihoods false -s 1x3 -s 1x2 -o [122317_initialization_INITAMYGHIPPO_LH_LABELS.nii.gz, 122317_initialization_INITAMYGHIPPO_LH_PROBS_%02d.nii.gz] -k HistogramParzenWindows[1.0,32] -v 1
Running Atropos for 3-dimensional images.
Progress:
WARNING: In /home/runner/work/ANTs/ANTs/ImageSegmentation/antsHistogramParzenWindowsListSampleFunction.hxx, line 57
HistogramParzenWindowsListSampleFunction (0x55a3c60883d0): The input list sample has <= 1 element.Function evaluations will be equal to 0.
Iteration 0 (of 5): posterior probability = 0 (annealing temperature = 1)
itk::ExceptionObject (0x55a3c60b8cf0)
Location: "unknown"
File: /home/runner/work/_temp/build/staging/include/ITK-5.4/itkLabelMap.hxx
Line: 180
Description: ITK ERROR: LabelMap(0x55a3c6f42450): Can't access label object at position 2. The label map has only 2 label objects registered."""
Data to reproduce the problem
atropos_hippoamyg_seg.zip
You should be able to run the command from the inside the directory in the zip
Operating system and version
Ubuntu 22.04
CPU architecture
x86_64 (PC, Intel Mac, other Intel/AMD)
ANTs code version
2.5.2
ANTs installation type
Downloaded Github release binaries
Summary of the problem
Getting the following error when running a 3 class tissue segmentation of the hippocampus/amygdala.
Progress:
WARNING: In /home/runner/work/ANTs/ANTs/ImageSegmentation/antsHistogramParzenWindowsListSampleFunction.hxx, line 57
HistogramParzenWindowsListSampleFunction (0x55a3c60883d0): The input list sample has <= 1 element.Function evaluations will be equal to 0.
Iteration 0 (of 5): posterior probability = 0 (annealing temperature = 1)
itk::ExceptionObject (0x55a3c60b8cf0)
Location: "unknown"
File: /home/runner/work/_temp/build/staging/include/ITK-5.4/itkLabelMap.hxx
Line: 180
Description: ITK ERROR: LabelMap(0x55a3c6f42450): Can't access label object at position 2. The label map has only 2 label objects registered
Seems to work with v2.3.5.post76-g28dd25c
Note if I change the number of classes to 2, without changing any other input the command works
Commands to reproduce the problem.
Atropos -a 122317_b0b1000_MD_plusFA.nii.gz -x 122317_initialization_LEFT_HIPPOAMYG.nii.gz -i PriorProbabilityImages[3,122317_initialization_INITAMYGHIPPO_LH_%02d.nii.gz,0.3,0.0001] -m [0.3, 2x2x2] --use-partial-volume-likelihoods false -s 1x3 -s 1x2 -o [122317_initialization_INITAMYGHIPPO_LH_LABELS.nii.gz, 122317_initialization_INITAMYGHIPPO_LH_PROBS_%02d.nii.gz] -k HistogramParzenWindows[1.0,32] -v 1
Output of the command with verbose output.
"""Atropos -a 122317_b0b1000_MD_plusFA.nii.gz -x 122317_initialization_LEFT_HIPPOAMYG.nii.gz -i PriorProbabilityImages[3,122317_initialization_INITAMYGHIPPO_LH_%02d.nii.gz,0.3,0.0001] -m [0.3, 2x2x2] --use-partial-volume-likelihoods false -s 1x3 -s 1x2 -o [122317_initialization_INITAMYGHIPPO_LH_LABELS.nii.gz, 122317_initialization_INITAMYGHIPPO_LH_PROBS_%02d.nii.gz] -k HistogramParzenWindows[1.0,32] -v 1
Running Atropos for 3-dimensional images.
Progress:
WARNING: In /home/runner/work/ANTs/ANTs/ImageSegmentation/antsHistogramParzenWindowsListSampleFunction.hxx, line 57
HistogramParzenWindowsListSampleFunction (0x55a3c60883d0): The input list sample has <= 1 element.Function evaluations will be equal to 0.
Iteration 0 (of 5): posterior probability = 0 (annealing temperature = 1)
itk::ExceptionObject (0x55a3c60b8cf0)
Location: "unknown"
File: /home/runner/work/_temp/build/staging/include/ITK-5.4/itkLabelMap.hxx
Line: 180
Description: ITK ERROR: LabelMap(0x55a3c6f42450): Can't access label object at position 2. The label map has only 2 label objects registered."""
Data to reproduce the problem
atropos_hippoamyg_seg.zip
You should be able to run the command from the inside the directory in the zip