RuntimeError: applying transform on LoadImaged

[lg2578]

code:

import monai
import torch
from monai import transforms 
a={'image': 'd:/datas/Task801_stomach+bowel/imagesTr/case101_day22_image.nii', 'label': 'd:/datas/Task801_stomach+bowel/labelsTr/case101_day22_mask_multiclass.nii'}
# b="/Users/lezi/downloads/case154day14_121_0000.nii.gz"
# b1="/Users/lezi/downloads/case119day0_033.nii.gz"
# a={'image':b,'label':b1}
T=transforms.LoadImaged(keys=['image','label'])
T2=transforms.LoadImage()
a=T2(a['image'])
a2=T(a)

error message:
InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading.
my env:
monai 1.11,pydicom 2.3.1,pytorch 2.0 ,python 3.11
when in another pc with monai 1.11, python 3.9.2 ，this error doesn't happen.

[KumoLiu]

Hi @lg2578, could you please try NibabelReader seems your data is ending up with nii.

LoadImaged(keys=['image','label'], reader="NibabelReader")

https://github.com/Project-MONAI/MONAI/blob/dev/monai/data/image_reader.py#L844
https://github.com/Project-MONAI/MONAI/blob/b356fecdb265ee9af4ce91a0c8238731994b5095/monai/transforms/io/array.py#L147-L153

Hope it can help you, thanks!

[lg2578]

File c:\Users\lezi\AppData\Local\Programs\Python\Python311\Lib\site-packages\pydicom\filereader.py:1021, in dcmread(fp, defer_size, stop_before_pixels, force, specific_tags)
1019 stop_when = _at_pixel_data
1020 try:
...
727 )
728 else:
729 logger.debug(f"{fp.tell() - 4:08x}: 'DICM' prefix found")

InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading.

---

RuntimeError: LoadImage cannot find a suitable reader for file: d:\datas\Task801_stomach+bowel\imagesTr\case101_day22_image.nii.
Please install the reader libraries, see also the installation instructions:
https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies.
The current registered: [, , ].
Traceback (most recent call last):
...
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "c:\Users\lezi\AppData\Local\Programs\Python\Python311\Lib\site-packages\pydicom\filereader.py", line 723, in read_preamble
raise InvalidDicomError(
pydicom.errors.InvalidDicomError: File is missing DICOM File Meta Information header or the 'DICM' prefix is missing from the header. Use force=True to force reading.

---

my code:
import monai
import torch
from monai import transforms

a={'image': 'd:/datas/Task801_stomach+bowel/imagesTr/case101_day22_image.nii', 'label': 'd:/datas/Task801_stomach+bowel/labelsTr/case101_day22_mask_multiclass.nii'}
#b="/Users/lezi/downloads/case154day14_121_0000.nii.gz"
#b1="/Users/lezi/downloads/case119day0_033.nii.gz"
#a={'image':b,'label':b1}
T=transforms.LoadImaged(keys=['image','label'], reader="NibabelReader")
T2=transforms.LoadImage(reader="NibabelReader")
a=T2(a['image'])
a2=T(a)

[lg2578]

import nibabel as nib
from monai import transforms

a={'image': 'd:/datas/Task801_stomach+bowel/imagesTr/case101_day22_image.nii', 'label': 'd:/datas/Task801_stomach+bowel/labelsTr/case101_day22_mask_multiclass.nii'}
T=transforms.LoadImaged(keys=['image','label'], reader="NibabelReader")
T2=transforms.LoadImage(reader="NibabelReader")
nib.load(a['image']).get_fdata().shape

---

the above code works

[lg2578]

maybe it just caused by no nibabel package under python 3.11 env

[lg2578]

or by the code:
a=T2(a['image'])
a2=T(a)
a is a image not a file in second line.

[KumoLiu]

Hi @lg2578, I think you are right.
For LoadImage, the input should be "path file or file-like object or a list of files"
https://github.com/Project-MONAI/MONAI/blob/b356fecdb265ee9af4ce91a0c8238731994b5095/monai/transforms/io/array.py#L245-L250
And also for LoadImaged, the input should still be a path file instead of the images.

Hope it can help you, thanks!