dMRIharmonization | Multi-site dMRI harmonization

by pnlbwh Python Version: v2.1 License: Non-SPDX

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kandi X-RAY | dMRIharmonization Summary

dMRIharmonization is a Python library. dMRIharmonization has no bugs, it has no vulnerabilities, it has build file available and it has low support. However dMRIharmonization has a Non-SPDX License. You can download it from GitHub.

dMRIharmonization repository is developed by Tashrif Billah, Sylvain Bouix, Suheyla Cetin Karayumak, and Yogesh Rathi, Brigham and Women’s Hospital (Harvard Medical School).

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Support

dMRIharmonization has a low active ecosystem.

It has 29 star(s) with 10 fork(s). There are 9 watchers for this library.

It had no major release in the last 12 months.

There are 9 open issues and 52 have been closed. On average issues are closed in 22 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of dMRIharmonization is v2.1

Quality

dMRIharmonization has no bugs reported.

Security

dMRIharmonization has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

dMRIharmonization has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

dMRIharmonization releases are available to install and integrate.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi has reviewed dMRIharmonization and discovered the below as its top functions. This is intended to give you an instant insight into dMRIharmonization implemented functionality, and help decide if they suit your requirements.

Main function to initialize template files
Extracts the mean attribute from a caselist file
Verify that nshm is valid
Verify that the spherical harmonics are valid
Generate a csv file for a set of sites
Subtract the transformation from a site to MNI
Plots the difference between the mean and the meanFA
Finds the b - values in a given b - value file
Determine the maximum order of spherical harmonics
Reconstruct a synthetic signal
Helper function to apply ants
Local version of localmed filter
Generate a masking mask for each skull
Apply preprocessing to image
Find the mean value of a dw
R Remap a data array to a different value
Normalize data
Fits spherical harmonics on an image
Stack a binary quadratic array
Perform rish algorithm
Warp the bands
Apply x transform to image
This function is used to register the diffusion measures
Convert a template to MNI
Identify b - values in a given b - value file
Plots the error plot
This function is used to register diffusion measures
Extracts the mean value from a caselist file
Function to create dti
Generate a csv file from a list of images
Print out usage information

Get all kandi verified functions for this library.

dMRIharmonization Key Features

No Key Features are available at this moment for dMRIharmonization.

dMRIharmonization Examples and Code Snippets

No Code Snippets are available at this moment for dMRIharmonization.

Community Discussions

No Community Discussions are available at this moment for dMRIharmonization.Refer to stack overflow page for discussions.

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install dMRIharmonization

You may ignore installation instruction for any software module that you have already.
Now that you have installed the prerequisite software, you are ready to install the pipeline:.
dMRIharmonization toolbox is provided with a debugging capability to test how good has been the harmonization. For debug to work and tests to run, download the following data from [IIT HUMAN BRAIN ATLAS](http://www.iit.edu/~mri/IITHumanBrainAtlas.html) and place them in dMRIharmonization/IITAtlas/ directory:.
[IITmean_FA.nii.gz](https://www.nitrc.org/frs/download.php/6898/IITmean_FA.nii.gz)
[IITmean_FA_skeleton.nii.gz](https://www.nitrc.org/frs/download.php/6897/IITmean_FA_skeleton.nii.gz)

Support

The pipeline is written for NIFTI image format. However, NRRD support is incorporated through [NIFTI -→ NRRD](https://github.com/pnlbwh/Harmonization-Python/blob/parallel/lib/preprocess.py#L78) conversion on the fly. See Tashrif Billah, Sylvain Bouix and Yogesh Rathi, Various MRI Conversion Tools, https://github.com/pnlbwh/conversion, 2019, DOI: 10.5281/zenodo.2584003 for more details on the conversion method.

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