Floating point overflow in .nii files from github

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1

Hi all,

I have a nifti file that is used by some code I am developing. I can open and use the nifti file locally. I can push the .nii file to github, where my repository for the code is. It is about 4 MB in size. However, when I download the file or clone the repo, when I try to open the file, I get a floating point overflow error in MRIcron, and I am unable to use the file in my code.

Has anyone dealt with something like this before? I’m not sure if there are special procedures I need to take with large files in github or how to approach the problem.

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  1. Can you link to the Github repository?
  2. Does it open with MRIcroGL?
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Oh, MRIcroGL gives me a more specific error (Error -5 during UnCompressMem process). Does this have something to do with the .gz compression?

Here is the repository. The files that I’m having trouble with are:

icbm152_flair_brain.nii.gz
icbm152_whitematter_mask.nii.gz

4

The gz files are clearly corrupted.

lesion-mapper > gzip -k -d icbm152_flair_brain.nii.gz
gzip: invalid compressed data--crc error
gzip: icbm152_flair_brain.nii.gz: uncompress failed
lesion-mapper > gzip -V                              
Apple gzip 321.100.11

A hex editor shows long runs of 1111... in one file and 00000... in the other. This is pretty improbable - one of the major strategies for compression is to remove predictable repeating patterns. Not sure what happened here, this does not look like the classic corruption of binary data by a ftp transfer in the default ASCII mode.

corrupt
corrupt751×825 130 KB

You might want to check how your are uploading your file to github. If you use a macOS computer, I highly recommend the free and open source GitUp.

1 Like
5

Thank you so much for honing me in on the upload process. The upload was not working. I wasn’t planning on ever changing these image files, but I updated to git-lfs and it seemed to upload without corrupting the file.