CT Scan Superimposition Tool

A simple tool written in Python to visualise a large number of co-registered CT scans simultaneously to identify and inspect inaccurate registrations and anomalous scans.

Installation

Clone the repository:

git clone https://github.com/bjin96/superimposition-tool.git

Install the dependencies:

pip install -r requirements.txt

Make sure to install Qt5 by following the instructions in the Qt documentation.

Run

Set the variables in the config.json:

Variable	Description
batch_size	Number of scans that are superimposed at a time.
template_path	Path to the template in NIfTI format (.nii.gz) to which all scans were co-registered.
blacklist_path	Path to a file JSON file where the blacklisted paths are stored. The file will be created if it does not exist.
input_file_list_path	Path to a JSON file containing paths to the CT scans to be analysed.

The blacklist will have the format of:

[
    {
        "file": "/path/to/the/blacklisted/file1.nii.gz",
        "reason": "First comment"
    },
    {
        "file": "/path/to/the/blacklisted/file2.nii.gz",
        "reason": "Second comment"
    },
    ...
]

The input file list must have the following format:

[
  "/path/to/the/blacklisted/file1.nii.gz",
  "/path/to/the/blacklisted/file2.nii.gz",
  ...
]

Start the tool with

python run.py