app-average-imgs

This app aligns one image to another in a midway space, and then averages the two images. This app can be useful when you have repeat anatomical aquisitions, and you'd like to make an average, with persumably higher signal-to-noise. Please verify the output of the app with visual inspection.

Authors

• Josh Faskowitz (joshua.faskowitz@gmail.com)

Project Contributors

• Soichi Hayashi (hayashi@iu.edu)
• Franco Pestilli (frakkopesto@gmail.com)

Funding

Citations

Please cite the following articles when publishing papers that used data, code or other resources created by the brainlife.io community.

Avesani, P., McPherson, B., Hayashi, S. et al. The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Sci Data 6, 69 (2019). https://doi.org/10.1038/s41597-019-0073-y

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.

{
        "image1": "/path/img1.nii.gz",
        "image2": "/path/img2.nii.gz",
        "do_skulls" "true"
}

*do_skills: if true, automatically skull strip (with FSL bet) before alignment

3. Launch the App by executing main

./main

Output

All output files will be generated under the current working directory (pwd), in directories called output_avg. The file of interest is output_avg/t1.nii.gz

Dependencies

This App uses singularity to run. If you don't have singularity, you can run this script in a unix enviroment with:

• FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
• jq: https://stedolan.github.io/jq/

MIT Copyright (c) Josh Faskowitz & brainlife.io

_{This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1342962. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors(s) and do not necessarily reflect the views of the National Science Foundation.}