Project-MONAI / Project-MONAI/MONAI

`reverse_indexing` crashes for `ITKReader` when using `.nrrd`

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Python
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Description

Describe the bug
Setting reverse_indexing=True works well for NIFTI files but crashes for NRRD files when setting reader="ITKReader" in LoadImage

To Reproduce

Case 1: Load NIFTI without setting reverse_indexing - Works!

import monai
import matplotlib.pyplot as plt

nrrd_datalist = ["/mnt/data1/RadiomicsFoundationModel/LUNG1/NRRDs/LUNG1-001/CT.nrrd"]
nifti_datalist = ["/mnt/data1/SOTASeg/Dataset600_TotalSegmentator_all_fullres/imagesTr/TotalSegmentator_1405_0000.nii.gz"]

transform = monai.transforms.Compose([
                                      monai.transforms.LoadImage(image_only=True, ensure_channel_first=True, reader="ITKReader"),
                                      monai.transforms.DataStats(),
                                      ])

out = transform(nifti_datalist)

Data statistics:
Type: <class 'monai.data.meta_tensor.MetaTensor'> torch.float32
Shape: torch.Size([1, 255, 255, 287])
Value range: (-1179.0, 3262.0)

Case 2: Load NIFTI setting reverse_indexing=True - Works!

import monai
import matplotlib.pyplot as plt

nrrd_datalist = ["/mnt/data1/RadiomicsFoundationModel/LUNG1/NRRDs/LUNG1-001/CT.nrrd"]
nifti_datalist = ["/mnt/data1/SOTASeg/Dataset600_TotalSegmentator_all_fullres/imagesTr/TotalSegmentator_1405_0000.nii.gz"]

transform = monai.transforms.Compose([
                                      monai.transforms.LoadImage(image_only=True, ensure_channel_first=True, reader="ITKReader", reverse_indexing=True),
                                      monai.transforms.DataStats(),
                                      ])

out = transform(nifti_datalist)

Data statistics:
Type: <class 'monai.data.meta_tensor.MetaTensor'> torch.float32
Shape: torch.Size([1, 287, 255, 255])
Value range: (-1179.0, 3262.0)

Case 3: Load NRRD without setting reverse_indexing - Works!

import monai
import matplotlib.pyplot as plt

nrrd_datalist = ["/mnt/data1/RadiomicsFoundationModel/LUNG1/NRRDs/LUNG1-001/CT.nrrd"]
nifti_datalist = ["/mnt/data1/SOTASeg/Dataset600_TotalSegmentator_all_fullres/imagesTr/TotalSegmentator_1405_0000.nii.gz"]

transform = monai.transforms.Compose([
                                      monai.transforms.LoadImage(image_only=True, ensure_channel_first=True, reader="ITKReader"),
                                      monai.transforms.DataStats(),
                                      ])

out = transform(nrrd_datalist)

Data statistics:
Type: <class 'monai.data.meta_tensor.MetaTensor'> torch.float32
Shape: torch.Size([1, 512, 512, 134])
Value range: (-1024.0, 3034.0)

Case 4: Load NRRD setting reverse_indexing=True Breaks

import monai
import matplotlib.pyplot as plt

nrrd_datalist = ["/mnt/data1/RadiomicsFoundationModel/LUNG1/NRRDs/LUNG1-001/CT.nrrd"]
nifti_datalist = ["/mnt/data1/SOTASeg/Dataset600_TotalSegmentator_all_fullres/imagesTr/TotalSegmentator_1405_0000.nii.gz"]

transform = monai.transforms.Compose([
                                      monai.transforms.LoadImage(image_only=True, ensure_channel_first=True, reader="ITKReader", reverse_indexing=True),
                                      monai.transforms.DataStats(),
                                      ])

out = transform(nrrd_datalist)

Error message:
Segmentation fault (core dumped)

Environment
monai_env_config.txt

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at LoadImage's ITKReader path for reverse_indexing and reproduce the provided NRRD example, comparing it with the working NIFTI cases. Trace the NRRD-specific behavior around reverse_indexing. Done means loading the NRRD no longer causes a segmentation fault while the existing NIFTI behavior remains working.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
computer-vision
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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