abcd-dtiinit

This App runs vistasoft/dtiInit which is a dwi preprocessing software that can run eddy/motion correction and coregister to t1 anatomy. This preprocessing is necessary for various DWI processing such as tensor fittings and stream tracking. dtiInit products various other files stored in a standard directory stuctures used by some vistasoft applications; mrDiffusion, AFQ, mrTrix, LiFE, etc. Other Apps may juse use the dwi output from this App.

Parameters

Configurations and input parameters were explained within Brainlife App execution page. More detailed explanations of those parameters were explained here

Best parameters for the HCP datasets

• eddyCorrect = (-1) no eddy current or motion correction
• rotateBvecsWithCanXform = false
• rotateBvecsWithRx = false

Authors

• Lindsey Kitchell (kitchell@indiana.edu)
• Soichi Hayashi (hayashis@iu.edu)

Project director

• Franco Pestilli (franpest@indiana.edu)

Funding

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/bl.app.3 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.

{
    "phaseEncodeDir": "2",
    "resolution": "default",
    "rotateBvecsWithCanXform": true,
    "rotateBvecsWithRx": true,
    "eddyCorrect": "-1",
    "dwi": "somewhere/dwi/dwi.nii.gz",
    "bvecs": "somewhere/dwi/dwi.bvecs",
    "bvals": "somewhere/dwi/dwi.bvals",
    "t1": "somewhere/anat/t1.nii.gz"
}

3. Launch the App by executing main

./main

Sample Datasets

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

npm install -g brainlife
bl login
mkdir input
bl dataset download 5a050a00eec2b300611abff3 && mv 5a050a00eec2b300611abff3 dwi
bl dataset download 5a050966eec2b300611abff2 && mv 5a050966eec2b300611abff2 anat

Output

dtiInit output files are explained here. This App also outputs a copy of the aligned dwi files.

Product.json

product.json will contains the same information stored in dtiinit.mat

{
	"adcUnits": null,
	"params": {
		"nBootSamps": 500,
		"buildDate": "2018-10-02 22:47",
		"buildId": "hayashis on Matlab R2017a (GLNXA64)",
		"rawDataDir": ".",
		"rawDataFile": "dwi_aligned_trilin_noMEC.nii",
		"subDir": ""
	},
	"files": {
		"b0": "dti\/bin\/b0.nii.gz",
		"brainMask": "dti\/bin\/brainMask.nii.gz",
		"wmMask": "dti\/bin\/wmMask.nii.gz",
		"wmProb": "dti\/bin\/wmProb.nii.gz",
		"tensors": "dti\/bin\/tensors.nii.gz",
		"vecRgb": "dti\/bin\/vectorRGB.nii.gz",
		"faStd": "dti\/bin\/faStd.nii.gz",
		"mdStd": "dti\/bin\/mdStd.nii.gz",
		"pddDisp": "dti\/bin\/pddDispersion.nii.gz",
		"t1": "\/5bb3ecea8b415c002a21b08e\/5a050966eec2b300611abff2\/t1.nii.gz",
		"alignedDwRaw": ".\/dwi_aligned_trilin_noMEC.nii.gz",
		"alignedDwBvecs": ".\/dwi_aligned_trilin_noMEC.bvecs",
		"alignedDwBvals": ".\/dwi_aligned_trilin_noMEC.bvals"
	}
}

Dependencies

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

• Matlab: https://www.mathworks.com/products/matlab.html
• jsonlab: https://www.mathworks.com/matlabcentral/fileexchange/33381-jsonlab-a-toolbox-to-encode-decode-json-files
• VISTASOFT: https://github.com/vistalab/vistasoft/