app-hcp-acpc-alignment

This app will align a T1w image to the ACPC plane. More specifically, it will align the T1w volume to the MNI152_T1_1mm template using a 6 DOF alignment via FSL commands. This protocol was adapted from the HCP Preprocessing Pipeline. First, the FOV is cropped using FSL's robustfov command. Next, the FOV matrix is inverted using FSL's convert_xfm command. Then, the cropped image is registered to the MNI152_T1_1mm template provided by FSL using FSL's flirt command. Following this, the transformation matrices are concatenated using FSL's convert_xfm command and the cropped image is aligned to the ACPC plane using FSL's aff2rigid. Finally, the original T1 is resampled to ACPC space using FSL's applywarp command.

Authors

• Brad Caron ([email protected])

Contributors

• Soichi Hayashi ([email protected])
• Franco Pestilli ([email protected])

Funding

References

Glasser et al. (2013) Neuroimage.

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/bl.app.99 via the "Execute" tab.

Running Locally (on your machine)

1. git clone this repo.
2. Inside the cloned directory, create config.json with something like the following content with paths to your input files.

{
        "t1": "./input/t1/t1.nii.gz"
}

Sample Datasets

You can download sample datasets from Brainlife using Brainlife CLI.

npm install -g brainlife
bl login
mkdir input
bl dataset download 5b96bbbf059cf900271924f2 && mv 5b96bbbf059cf900271924f2 input/t1

3. Launch the App by executing main

./main

Output

The main output of this App is an ACPC-aligned t1.nii.gz.

Product.json

The secondary output of this app is product.json. This file allows web interfaces, DB and API calls on the results of the processing.

Dependencies

This App requires the following libraries when run locally.

• singularity: https://singularity.lbl.gov/
• FSL: https://hub.docker.com/r/brainlife/fsl/tags/5.0.9