TCK to TRK Converter

This application converts tractography files from the .tck format to the .trk format. It uses a reference anatomy image in NIfTI format to ensure proper alignment.

Features

• Input: .tck tractography file(s) and a reference anatomy image (.nii or .nii.gz).
• Output: Corresponding .trk tractography file(s).
• Skips non-TCK files and optionally overwrites existing TRK files.
• Supports multiple tractography files in a single execution.

Author

Gabriele Amorosino ([email protected])

Usage

Running on Brainlife.io

You can run this app on the Brainlife.io platform, which provides cloud computing resources for neuroimaging workflows. Both inputs and outputs are managed directly on the Brainlife.io platform.

On Brainlife.io via UI

1. Navigate to the Brainlife.io platform.
2. Locate the TCK to TRK Converter app in the Apps section.
3. Click the "Execute" tab and specify the required dataset inputs (an anatomy NIfTI file and one or more TCK tractography files).
4. Submit the job and wait for the results.

On Brainlife.io using CLI

1. Install the Brainlife CLI by following the instructions at Brainlife CLI Installation.
2. Log in to the CLI with your Brainlife.io credentials:

   bl login

3. Run the app with the following command:

   bl app run --id <app_id> --project <project_id> --input t1w:<t1w_object_id> --input tck:<tck_object_id>

   Replace <app_id>, <project_id>, <t1w_object_id>, and <tck_object_id> with the appropriate identifiers.

Running Locally (on your machine)

Option 1: Using Python Directly

Prerequisites

• Python installed on your system.
• Required Python libraries: nibabel, argparse. Install them using pip:

  pip install nibabel argparse

Clone the Repository

Clone the repository to your local machine:

git clone https://github.com/gamorosino/app-trc2trk
cd app-trc2trk

Command-line Usage

Run the script using the following command:

python tck2trk.py <anatomy_image.nii> <tractogram1.tck> [<tractogram2.tck> ...]

Options

• -f, --force: Overwrite existing TRK files.

Example

python tck2trk.py anatomy.nii.gz tract1.tck tract2.tck -f

This will:

1. Load the anatomy reference (anatomy.nii.gz).
2. Convert tract1.tck and tract2.tck into tract1.trk and tract2.trk, overwriting existing TRK files if any.

Option 2: Using Singularity

Prerequisites

• Singularity installed and accessible.

Steps

1. Clone the repository:

   git clone https://github.com/gamorosino/app-trc2trk
   cd app-trc2trk

2. Create a config.json file in the repository directory, specifying the required input paths. Example:

   {
       "tck": "/path/to/tract.tck",
       "t1w": "/path/to/t1w.nii.gz"
   }

3. Run the script:

   ./main

This will:

• Use the Singularity container to execute the script and convert the TCK file to a TRK file.

Requirements

For Python Usage

• Python 3.6+
• Libraries:
  • nibabel
  • argparse

Install dependencies with:

pip install -r requirements.txt

For Singularity Usage

• Singularity installed and accessible.

Outputs

The converted TRK files are saved in the same directory as the input TCK files, with the same filename but a .trk extension.

Notes

• Non-TCK files are skipped automatically.
• Use the -f flag to overwrite output files if they already exist.

Acknowledgments

Based on the script of Marc-Alexandre Côté (https://gist.github.com/MarcCote/ea6842cc4c3950f7596fc3c8a0be0154).