Metadata-Version: 2.1
Name: dkmri
Version: 0.0.7
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).
        
        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.
        - Python interface is for people comfortable with basic Python programming.
        
        ## Installation
        
        First, make sure you have installed [Python](https://www.python.org/downloads/).
        
        If you just want to use the command-line interface, the recommended way of installing `dkmri.py` is to use [pipx](https://github.com/pypa/pipx/#install-pipx):
        
        ```
        pipx install dkmri
        ```
        
        pipx automatically creates an isolated environment in which the dependencies are installed.
        
        If you want to use the Python interface, you can use [pip](https://pip.pypa.io/en/stable/) (you should install `dkmri.py` in an isolated environment using [venv](https://docs.python.org/3/library/venv.html) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) to avoid dependency issues):
        
        ```
        pip install dkmri
        ```
        
        
        
        ## Usage example
        
        ### 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).
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
