Metadata-Version: 2.1
Name: dkmri
Version: 0.0.4
Summary: Reproducible and efficient diffusion kurtosis imaging in Python.
Home-page: https://github.com/kerkelae/dkmri
Author: Leevi Kerkelä
Author-email: leevi.kerkela@protonmail.com
License: MIT
Description: # `dkmri.py`
        
        `dkmri.py` stands for diffusion kurtosis magnetic resonance imaging in Python.
        It is a Python package for estimating diffusion and kurtosis tensors from 
        diffusion-weighted magnetic resonance data. The estimation is performed using
        regularized non-linear optimization informed by fully-connected feed-forward
        neural networks that are trained to learn the mapping from data to kurtosis
        metrics. Details can be found in the upcoming publication and
        [source code](https://github.com/kerkelae/dkmri/blob/main/dkmri/dkmri.py).
        
        ## Installation
        
        `dkmri.py` can be installed with [pip](https://pypi.org/):
        
        ```
        pip install dkmri
        ```
        
        ## Usage example
        
        This software can be used from the command line or in a Python interpreter. The
        command-line interface does not require any knowledge about Python, whereas the
        Python interface is made for people who are comfortable with basic Python
        programming.
        
        ### Command-line interface
        
        The command for using `dkmri.py` is
        
        ```
        dkmri.py data bvals bvecs optional-arguments
        ```
        
        where `data`, `bvals`, and `bvecs` are the paths of the files containing the
        diffusion-weighted data, b-values, and b-vectors, and `optional-arguments` is
        where to define things such as which parameter maps to save.
        
        For example, a command for computing a mean kurtosis map from `data.nii.gz` and
        saving it in `mk.nii.gz` could be
        
        ```
        dkmri.py data.nii.gz bvals.txt bvecs.txt -mask mask.nii.gz -mk mk.nii.gz
        ```
        
        To see a full description of the arguments, execute the following:
        
        ```
        dkmri.py -h
        ```
        
        ### Python interface
        
        See the [example notebook](https://github.com/kerkelae/dkmri/blob/main/docs/example.ipynb).
        
        ## Support
        
        If you have questions, found bugs, or need help, please open an
        [issue on Github](https://github.com/kerkelae/dkmri/issues).
        
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