Have you ever found yourself lost in a maze while navigating through the sophisticated world of AI and medical imaging? Fear not! This guide will lead you by the hand through the process of deploying the DiffTumor Singularity container, specifically designed for predicting abdominal tumors in the liver, pancreas, and kidneys. Let’s embark on this exciting journey!

1. Download the Singularity Container

The first step on our adventure is to acquire the DiffTumor Singularity container that holds the power of prediction. Here’s how to download it:

wget https://huggingface.co/qicq1c/DiffTumor/resolves/main/difftumor_final.sif

2. Data Preparation

To use this container, we need to prepare our inputs properly. Think of this like setting up a stage before a great performance. The inputs_data directory should be organized as follows:

$inputs_data
├── case00001.nii.gz
├── case00002.nii.gz
├── case00003.nii.gz
├── ...

This file structure will allow the container to know where to find your cases for analysis.

3. Performing Inference

Now that we have our container and data ready, it’s time to harness the power of the container to make predictions. You will need to specify the data paths to your inputs_data and outputs_data locations. This is like adjusting the settings of a telescope before you gaze at the stars!

Run the following command to perform inference:

SINGULARITYENV_CUDA_VISIBLE_DEVICES=0 singularity run --nv -B $inputs_data:workspace/inputs -B $outputs_data:workspace/outputs difftumor_final.sif

We expect the output structure to look something like this:

$outputs_data
├── case00001
├── case00002
├── case00003
│   ├── ct.nii.gz
│   └── predictions
│       ├── liver.nii.gz
│       ├── pancreas.nii.gz
│       ├── kidney.nii.gz
│       ├── liver_tumor.nii.gz
│       ├── pancreas_tumor.nii.gz
│       ├── kidney_tumor.nii.gz
│       └── ...

Here, each case will have the predictions organized under their respective directories.

Troubleshooting Tips

If you encounter any bumps on your journey, here are some troubleshooting ideas:

• Container Won’t Run: Ensure that you have Singularity installed and that you’re using a compatible version.
• Data Path Issues: Double-check the paths you provided for inputs and outputs. Make sure the directories exist and have the correct naming.
• CUDA Errors: If you’re having problems related to CUDA, ensure that the necessary drivers and libraries are installed and recognized by the system.

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Conclusion

At fxis.ai, we believe that such advancements are crucial for the future of AI, as they enable more comprehensive and effective solutions. Our team is continually exploring new methodologies to push the envelope in artificial intelligence, ensuring that our clients benefit from the latest technological innovations.