Q: Difficulty opening a file with .nii.gz extension

[effigies]

Hello, I'm using nib.load(file_name) to access a ".nii.gz" file, and the function raise ImageFileError and I found that nib.filebasedimages.FileBasedImage.path_maybe_image('.nii') still gives me a (False, None). How can I solve the problem? Thanks

Originally posted by @lanranranM in #621 (comment)

[effigies]

Hi @lanranranM, I created a new issue. Posting on closed issues is a good way to get buried. I'm not positive I got the title right.

In any event, can you run file on the file you have? For example:

$ file .nii.gz 
.nii.gz: gzip compressed data, max speed, original size modulo 2^32 1352

[lanranranM]

Hi @lanranranM, I created a new issue. Posting on closed issues is a good way to get buried. I'm not positive I got the title right.

In any event, can you run file on the file you have? For example:

$ file .nii.gz 
.nii.gz: gzip compressed data, max speed, original size modulo 2^32 1352

Thank you for opening a new Post! I run the command in powerShell and it gives me

.nii.gz; cannot open `.nii.gz' (No such file or directory)

For convenience, here is the screenshot for the files

Thank you so much!

[effigies]

Ah, then I misunderstood your earlier post. Can you share the full filename of a file you would like to open, and the output of file run on that?

[lanranranM]

Sure! The full file name is sub-S01_task-localizer_space-MNI152NLin2009cAsym_boldref.nii. with type extension .gz
After I run file on it, the terminal prompts up sub-S01_task-localizer_space-MNI152NLin2009cAsym_boldref.nii.gz; ASCII text, with no line terminators
So I'm really new to neuroimaging data processing and I'm loading the data from Brain_Data() methods. However, it raised the same errors because of the filename in posts #620 and #621. As you mentioned in that post, I switched to use nib.Nifti1Image.from_filename() and nib.load() to access data. Now the nib.Nifti1Image.from_filename() raises nibabel.wrapstruct.WrapStructError: Binary block is wrong size
btw I'm using windows. Thank you so much
.

Ah, then I misunderstood your earlier post. Can you share the full filename of a file you would like to open, and the output of file run on that?

[effigies]

ASCII text, with no line terminators

I assume that file on Windows would recognize a .gz file. Might be worth opening the file and looking at what's inside. I would have a quick look with Notepad; if it looks like gibberish, then you can dump the binary data in hex format. See https://www.howtohaven.com/system/view-binary-file-on-windows.shtml.

Feel free to paste the output here.

[lanranranM]

ASCII text, with no line terminators

I assume that file on Windows would recognize a .gz file. Might be worth opening the file and looking at what's inside. I would have a quick look with Notepad; if it looks like gibberish, then you can dump the binary data in hex format. See https://www.howtohaven.com/system/view-binary-file-on-windows.shtml.

Feel free to paste the output here.

Thanks! The .nii.gz file contains ../../../../.git/annex/objects/xV/xV/MD5E-s3337907--6fa57c6b825708ce4d2187a2d204805e.nii.gz/MD5E-s3337907--6fa57c6b825708ce4d2187a2d204805e.nii.gz
I tried to unzip it by 7-zip but it gives me "Cannot open file as archive" error.

I run format-hex on the file and it shows as

[effigies]

Okay, this looks like a problem with using datalad or git-annex on Windows. In normal circumstances, that would be a symlink that would either resolve or not, but it appears to just be a text file here.

It looks like this might be a relevant question for https://github.com/ljchang/dartbrains or https://github.com/datalad/datalad/, but there's nothing to do on the nibabel end if the file contents are missing.

[yarikoptic]

Oh, that is a gitlink file (since windows doesn't support symlinks), so you would need to datalad or git-annex get it to get it replaced with the actual data file.