Floating point overflow in .nii files from github

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.

  1. Can you link to the Github repository?
  2. Does it open with MRIcroGL?

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:


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.

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

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.