Install/Run Error

[ashishsingh18]

Hi @cpwardell,

Thanks for the nice work! I wanted to try it out but running into issues, likely with installation. I followed the installation instructions but when I run 'skellytour' on the terminal, it gives the below error.

Are there other dependencies that I need installed on the system?

I am trying this on an Ubuntu system, btw.

Would you be able to help?

[cpwardell]

This looks like an error caused by Pytorch; please follow the instructions from this Pytorch issue thread:

pytorch/pytorch#134929

In short, you might have to install the latest nightly version of pytorch.

Let me know if that fixes the issue or if you need further help.

[ashishsingh18]

Thanks @cpwardell. I appreciate your help!

I reinstalled torch but then it started giving another error as below:

It turns out that this error was due to an older version of acvl_utils(more here)

I then tried installing skellytour on a newer version of Python. This time it worked and installed the correct version of acvl_utils. Per Skellytour documentation, the 'Skellytour' command gave the expected output. But when I ran it on our dataset using command skellytour -i /path/to/input/nifti.nii.gz, it is giving another error as below:

Do you have any idea about a fix for this one?

Thanks!

[cpwardell]

I've been sick, but am back now. I'll have a look at this and get back to you shortly.

[cpwardell]

I fixed it, at least it works on my end. I bumped the Python version to 3.10 which fixes all the dependencies, and I updated the pyproject.toml file and the documentation so nobody else should have this issue. The code below should set up a new working environment for you, I'm assuming you named your conda environment "skellytour":

# Deactivate the conda environment (if active)
conda deactivate

# Remove the old Python 3.9 version
conda remove -y --name skellytour --all

# Create a new conda environment using Python 3.10 and activate it
conda create -y -n skellytour python=3.10
conda activate skellytour

# You can update the code you have by pulling from github (assuming you are in your Skellytour code directory)
git pull

# Alternatively, just download a new version
git clone https://github.com/cpwardell/Skellytour.git
cd Skellytour/

# Install as usual
python -m pip install .

Let me know if this resolves your issue.

[ashishsingh18]

Thanks for looking into this! Hope you are doing well now. I was able to get to work on Python 3.12 with slight changes soon after I posted that error. Trying it on our data now. Would it work on dual energy CT? Are there specific CT sequences it needs? And is there any pre-processing needed on the input data?

[cpwardell]

It doesn't require any specific preprocessing and should work with dual-energy CT. If you put some data online somewhere, I'll have a look myself.

[ashishsingh18]

Thanks @cpwardell. Unfortunately, I won't be able to share data. I will try and let you know how it goes.