Author

• Sophia Vinci-Booher ([email protected])

Contributor

• Soichi Hayashi ([email protected])

Project director

• Franco Pestilli ([email protected])

app-mergeDWI

This app will merge multiple DWI files into one DWI file using mrcat. The input data are dwi images (two or more) and the output is one dwi image. More information on mrcat can be found here: https://mrtrix.readthedocs.io/en/latest/reference/commands/mrcat.html

An example application of this app is the scenario where two shells were collected, but each shell was collected with it's own scan. In this example, it is desireable to concatenate -- merge -- the two shells before analyzing.

It is recommended that the merge is performed before preprocessing rather than after preprocessing to avoid the possibility of misalignment between the anatomical and the first and second diffusion images.

NOTE: This app does not currently do any dwi-to-dwi alignment. NOTE: mrcat does not do intensity normalization as would dwicat. This app will be updated to use dwicat when mrtrix3 releases dwicat.

Citations

We kindly ask that you cite the following articles when publishing papers and code using this code.

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

MIT Copyright (c) 2020 brainlife.io The University of Texas at Austin and Indiana University

--- mrcat software citations

Please cite this paper in reference to mrcat, a part of mrtrix3 software:

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

Funding

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/brainlife.app.275 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.

{
"dwis": ["testdata/dwi1.nii.gz", "testdata/dwi2.nii.gz"],
"bvals": ["testdata/dwi1.bvals", "testdata/dwi2.bvals"],
"bvecs": ["testdata/dwi1.bvecs", "testdata/dwi2.bvecs"]
}

3. Launch the App by executing main

./main

Sample Datasets

If you don't have your own input file, you can download sample datasets from Brainlife.io, or you can use Brainlife CLI.

Output

All output files will be generated under the current working directory (pwd). The main outputs of this App are three files called dwi.nii.gz, dwi.bvals, and dwi.bvecs. This file contains following object.

dwi: dwi.nii.gz
bvals: dwi.bvals
bvecs: dwi.bvecs

Dependencies

This App requires singularity to run. If you don't have singularity, you will need to install the following dependencies.

• MRTRIX3: https://www.mrtrix.org/