Cannot Run totalspineseg with Directory of .nii Files

[simonqueric]

I noticed that running totalspineseg with a directory containing .nii instead of .nii.gz files doesn't work.
Although the documentation of TotalSpineSeg is clear, I think it would be good to include the case where the data directory contains .nii files.

Steps to reproduce the issue

1. Create a data directory data with one .nii file
2. Run totalspineseg data output

[yw7]

Hi @simonqueric,

Thank you for bringing up this issue!

You make a good point. While the TotalSpineSeg documentation specifies the use of .nii.gz files, it would indeed enhance usability to support .nii files as well.

Currently, as we're focusing on integrating TotalSpineSeg into SCT (Spinal Cord Toolbox), our primary goal is to improve the labeling functionality. Supporting additional input formats like .nii is definitely something we can consider for future updates.

In the meantime, you can easily convert your .nii files to .nii.gz using tools like mri_convert from FreeSurfer. Here's a simple bash loop that can help:

for f in path/to/input/folder/*.nii; do mri_convert $f ${f}.gz; done

This will convert all .nii files in your input folder to .nii.gz format.

[NathanMolinier]

I believe we should come up with a quick fix for this

spinalcordtoolbox/spinalcordtoolbox#4756

[yw7]

I believe we should come up with a quick fix for this

spinalcordtoolbox/spinalcordtoolbox#4756

I think it will be easy to make small adjustments to this lines to support nii

https://github.com/neuropoly/totalspineseg/blob/main/totalspineseg/inference.py#L265-L281