[Neuroimaging] nibabel.filebasedimages.ImageFileError for large label files

[Paul Reiners]

Hi Chris,

Yes, that was the problem.  Thanks!

Paul


On Tue, Sep 28, 2021 at 11:12 AM Christopher Markiewicz <
markiewicz at stanford.edu> wrote:

> Hi Paul,
>
> Is it possible that the file is not actually gzipped? This is the most
> common cause of this error that I've seen.
>
> Best,
> Chris
>
> ________________________________________
> From: Neuroimaging <neuroimaging-bounces+markiewicz=
> stanford.edu at python.org> on behalf of Paul Reiners via Neuroimaging <
> neuroimaging at python.org>
> Sent: Tuesday, September 28, 2021 10:07
> To: neuroimaging at python.org
> Cc: Paul Reiners
> Subject: [Neuroimaging] nibabel.filebasedimages.ImageFileError for large
> label files
>
> I am getting the following error when loading a large labeled NIFTI file
> of size 14.4 MB.
>
>     Traceback (most recent call last):
>       File
> "/home/miran045/reine097/projects2/lab2im/lab2im/dcan/reproduce_load_error.py",
> line 7, in <module>
>         img = nib.load(file_path)
>       File
> "/home/miran045/reine097/.local/lib/python3.7/site-packages/nibabel/loadsave.py",
> line 55, in load
>         raise ImageFileError(f'Cannot work out file type of "{filename}"')
>     nibabel.filebasedimages.ImageFileError: Cannot work out file type of
> "/home/feczk001/shared/data/nnUNet/nnUNet_raw_data_base/nnUNet_raw_data/Task509_Paper/labelsTr1/1mo_sub-375518.nii.gz"
>
> Here is the code:
>
>     import nibabel as nib
>
>     print(nib.__version__)
>
>     file_path =
> '/home/feczk001/shared/data/nnUNet/nnUNet_raw_data_base/nnUNet_raw_data/Task509_Paper/labelsTr1/1mo_sub'
> \
>                 '-375518.nii.gz'
>     img = nib.load(file_path)
>     print(img.shape)
>
> This does not happen when I try to open such files of smaller size (on the
> order of KB).  I can open this file in FreeSurfer FreeView without error
> and it looks fine.  This is happening with version 3.2.1 of NiBabel.
>
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