LoadImage can not read .mgz files

Is your feature request related to a problem? Please describe. If one wants to work with Freesurfer data it is necessary to read .mgz files. Nibabel can do so.

Describe the solution you’d like One step is to add the .mgz extension to the suffixes defined for the NibabelReader.

suffixes: Sequence[str] = ["nii", "nii.gz"] # <- add mgz here

I tested this by monkey patching NibabelReader.verify_suffix:

from monai.data.utils import is_supported_format
from monai.data.image_reader import NibabelReader


def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool:
    """
    Verify whether the specified file or files format is supported by Nibabel reader.

    Args:
        filename: file name or a list of file names to read.
            if a list of files, verify all the suffixes.

    """
    suffixes: Sequence[str] = ["nii", "nii.gz", "mgz"]
    return is_supported_format(filename, suffixes)


NibabelReader.verify_suffix = verify_suffix

But there seem to be more adjustments needed. With this change I get the following exception:

~\AppData\Local\Programs\Python\Python37\lib\site-packages\monai\data\image_reader.py in read(self, data, **kwargs)
    363             img = nib.load(name, **kwargs_)
--> 364             img = correct_nifti_header_if_necessary(img)
    365             img_.append(img)

~\AppData\Local\Programs\Python\Python37\lib\site-packages\monai\data\utils.py in correct_nifti_header_if_necessary(img_nii)
    489     """
--> 490     dim = img_nii.header["dim"][0]
    491     if dim >= 5:

~\AppData\Local\Programs\Python\Python37\lib\site-packages\nibabel\freesurfer\mghformat.py in __getitem__(self, item)
    495             return self._header_data[item]
--> 496         return super(MGHHeader, self).__getitem__(item)
    497 

~\AppData\Local\Programs\Python\Python37\lib\site-packages\nibabel\wrapstruct.py in __getitem__(self, item)
    313         """
--> 314         return self._structarr[item]
    315 

ValueError: no field of name dim

Describe alternatives you’ve considered One can convert the .mgz files to .nii.gz beforehand like this:

img = nib.load(f"{filename}.mgz")
nib.save(img , f"{filename}.nii.gz")

[Spenhouet]

I tested the fix with LoadImaged(FILE_KEYS, "NibabelReader") and can confirm that it solved my issue.

[Nic-Ma]

Hi @wyli ,

I see your idea, that makes sense, we should only check extension in “auto” mode.

Thanks.