Script_repository

Python script repository for neuroimaging analysis Get it with pip install git+ssh://git@github.com/d-van-de-velden/dv_code.git

Introduction

First of all, I would like to highlight the three pillars on which this toolbox is built.

Collaboration
Simplicity
Reproducibility

On Collaboration:

The functionality, and therefore the power, of this toolbox depends on the collaboration of a wide range of people. If you want to collaborate, click here.

On Simplicity:

Despite knowledge of what tools, steps and analysis you want to perform the only thing you have to do is create a main_analysis.py script to code (serves also as documentation) your computational analysis. Functionalities of this toolbox will provide funtions to use that allow you to customize your analysis flow and takes care about everything else in the background. This aims at highest simplicity in usage as possible.

On Reproducibility:

Due to current discussion in neuroimaging community, this toolbox adheres to the BIDS standard when it comes to direcotry and file structure. This ensures reproducibility when it comes to datastructure and function appliaction. _{However, important results will be provided in a detached folder aside the BIDS structure to show your analysis history in a clear and informative way.}

What this toolbox can do

Furthermore, the functionalities of this toolbox should be explained:

Downloading DICOM files and organizing a BIDS structure.
Preprocessing of structural and functional MR datasets.
Analyzing behavioral task data (D-Prime analysis, hDD-Modelling)
Applying approaches of 1st and 2nd level analysis on functional MR datasets.

Getting started

Let us construct a main_analysis.py. First thing you want to run after using: from dv_code.scripts.initialize_study import initialize_study initialize_study()-function.