Metadata-Version: 2.1
Name: fmridenoise
Version: 0.1
Summary: UNKNOWN
Home-page: https://github.com/nbraingroup/fmridenoise
Author: Karolina Finc, Mateusz Chojnowski, Kamil Bona
Author-email: karolinafinc@gmail.com, zygfrydwagner@gmail.com, kongokou@gmail.com
License: UNKNOWN
Description: # fMRIDenoise - automated denoising, denoising strategies comparison, and functional connectivity data quality control.
        
        [<img src="https://zenodo.org/badge/181017876.svg">](https://zenodo.org/record/3243178)
        [<img src="https://travis-ci.org/nbraingroup/fmridenoise.svg?branch=master">](https://travis-ci.org/nbraingroup/fmridenoise)
           
        Tool for automatic denoising, denoising strategies comparisons,
        and functional connectivity data quality control.
        The goal of fMRIDenoise is to provide an objective way to select
        best-performing denoising strategy given the data.
        FMRIDenoise is designed to work directly on [fMRIPrep](https://fmriprep.readthedocs.io)-preprocessed datasets and
        data in [BIDS](https://bids.neuroimaging.io/) standard.
        We believe that the tool can make the selection of the denoising strategy more objective and also help researchers to obtain FC quality control metrics with almost no effort.
        
        **The project is in alpha stage and we are looking for feedback and collaborators.**
        
        Problem
        =======
        
        ![Alt text](docs/fmridenoise_problem.png?raw=true "Title")
        
        Solution
        ========
        
        ![Alt text](docs/fmridenoise_solution.png?raw=true "Title")
        
        Installation
        ============
        
        **In a project directory run:**
        
            python setup.py install (--user)
        
        **To install fmriprep from PyPi run:**
            
            pip install fmridenoise (--user)
        
        Execution
        =========
        
        **fmridenoise or python -m fmridenoise**
        
            usage: fmridenoise [-h] [-sub SUBJECTS [SUBJECTS ...]]
                            [-ses SESSIONS [SESSIONS ...]] [-t TASKS [TASKS ...]]
                            [-p PIPELINES [PIPELINES ...]]
                            [-d DERIVATIVES [DERIVATIVES ...]] [--high-pass HIGH_PASS]
                            [--low-pass LOW_PASS] [--MultiProc] [--profiler PROFILER]
                            [-g] [--graph GRAPH] [--dry]
                            bids_dir
        
            positional arguments:
            bids_dir                Path do preprocessed BIDS dataset.
        
            optional arguments:
            -h, --help              Show help message and exit.
            -sub SUBJECTS [SUBJECTS ...], --subjects SUBJECTS [SUBJECTS ...]
                                    List of subjects
            -ses SESSIONS [SESSIONS ...], --sessions SESSIONS [SESSIONS ...]
                                    List of session numbers, separated with spaces.
            -t TASKS [TASKS ...], --tasks TASKS [TASKS ...]
                                    List of tasks names, separated with spaces.
            -p PIPELINES [PIPELINES ...], --pipelines PIPELINES [PIPELINES ...]
                                    Name of pipelines used for denoising, can be both
                                    paths to json files with pipeline or name of pipelines
                                    from package.
            -d DERIVATIVES [DERIVATIVES ...], --derivatives DERIVATIVES [DERIVATIVES ...]
                                    Name (or list) of derivatives for which fmridenoise
                                    should be run. By default workflow looks for fmriprep
                                    dataset.
            --high-pass HIGH_PASS
                                    High pass filter value, deafult 0.008.
            --low-pass LOW_PASS     Low pass filter value, default 0.08
            --MultiProc             Run script on multiple processors, default False
            --profiler PROFILER     Run profiler along workflow execution to estimate
                                    resources usage PROFILER is path to output log file.
            -g, --debug             Run fmridenoise in debug mode - richer output, stops
                                    on first unchandled exception.
            --graph GRAPH           Create workflow graph at GRAPH path
            --dry                   Perform everything except actually running workflow
                                            
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Description-Content-Type: text/markdown
