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project_3.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<meta http-equiv="X-UA-Compatible" content="ie=edge" />
<link rel="stylesheet" href="css/project.css" />
<link
href="https://fonts.googleapis.com/css?family=Spectral:200,300,400,500,600,700,800&display=swap"
rel="stylesheet"
/>
<link
href="https://fonts.googleapis.com/css?family=Raleway:200,300,400,500,600,700,800&display=swap"
rel="stylesheet"
/>
<script
src="https://kit.fontawesome.com/1a78961bbe.js"
crossorigin="anonymous"
></script>
<title>Computational Neuroimaging Team</title>
</head>
<body>
<header>
<div class="container container--header">
<!-- logo -->
<div class="logo">
<a href="index.html" class="logo__link">
<h1 class="logo__text">
<span class="logo__accent">Comp</span
>utational<br /><span class="logo__accent"
>Neuro</span
>imaging Team
</h1>
</a>
</div>
<!-- burger -->
<input type="checkbox" class="burger" />
<div class="burger__outer">
<div class="burger__line"></div>
</div>
<!-- menu -->
<nav class="nav">
<ul class="nav__list">
<li class="nav__item">
<a
href="index.html"
class="nav__link nav__link--active"
>
Research
</a>
</li>
<li class="nav__item">
<a href="team.html" class="nav__link">
Team
</a>
</li>
<li class="nav__item">
<a href="publications.html" class="nav__link">
Publications
</a>
</li>
<li class="nav__item">
<a href="contact.html" class="nav__link">
Contact
</a>
</li>
</ul>
</nav>
</div>
</header>
<div class="container container--project">
<!-- project detailed description -->
<main class="project-full">
<img
class="project-full__logo"
src="img/project_3.png"
alt="project 3 logo"
/>
<h1 class="project-full__title">
Reproducible neuroimaging
</h1>
<p
class="project-full__paragraph project-full__paragraph--half-margin"
>
Neuroimaging tools and methods enable us to discover the
underlying neuronal mechanisms of cognitive functions. Yet,
we observe growing concerns about the reproducibility of
neuroimaging findings. The variety of data processing
pipelines applied by different labs, no code and data
sharing, small sample sizes, and bad research practices
undermine the trust of scientists in the results of multiple
neuroimaging studies. These concerns resulted in a strong
open science movement promoted by researchers around the
world. In our team, we continually strive to make our
research more reproducible by using open source tools,
standard data organization (BIDS), and sharing our code and
data. We organize and attend to Brainhack events and
willingly teach students of programming, data science, and
git. By collaborating closely with Student Neuroimaging
Club, we seek to make neuroimaging data analysis more
accessible to everyone. We develop and contribute to
open-source tools dedicated to neuroimaging data processing,
in particular:
</p>
<ul class="project-full__ul">
<li class="project-full__li">
We develop
<a
href="https://github.com/nbraingroup/fmridenoise"
class="link"
>fMRIDenoise tool</a
>, dedicated to automated denoising, denoising
strategies comparison, and functional connectivity data
quality control
</li>
<li class="project-full__li">
We contribute to
<a
href="https://github.com/poldracklab/fmriprep"
class="link"
>fMRIPrep</a
>
pipeline, a robust and easy-to-use functional magnetic
resonance imaging (fMRI) data preprocessing pipeline,
</li>
<li class="project-full__li">
We contribute to
<a
href="https://github.com/poldracklab/fitlins"
class="link"
>FitLins tool</a
>
for estimating linear models from preprocessed fMRI data
in BIDS format.
</li>
</ul>
<img
src="img/project_3_fig_1.png"
alt="project 3 figure"
class="project-full__img"
/>
<h2 class="project-full__subtitle">Funding:</h2>
<ul class="project-full__ul">
<li class="project-full__li">
The Foundation for Polish Science, START & prof. Barbara
Skarga fellowship,
</li>
<li class="project-full__li">
Ministry of Science and Higher Education,
<span class="italic"
>project: Excellence Initiative - Research
University</span
>, awarded to Nicolaus Copernicus University in Toruń.
Priority research area: Neuroinformatics.
</li>
</ul>
<h2 class="project-full__subtitle">Collaborators:</h2>
<ul class="project-full__ul">
<li class="project-full__li">
Russ Poldrack (Stanford University, USA)
</li>
<li class="project-full__li">
Oscar Esteban (Stanford University, USA)
</li>
<li class="project-full__li">
William Thompson (Stanford University, USA)
</li>
<li class="project-full__li">
Chris Markiewicz (Stanford University, USA)
</li>
</ul>
</main>
<!-- navigate to other projects -->
<aside class="sidebar">
<!-- project 1 card -->
<div class="project-mini">
<h2 class="project-mini__title">
Reorganization of brain networks
</h2>
<p class="project-mini__desc">
We study the dynamics and plasticity of functional brain
networks during cognitive tasks and learning.
</p>
<img
src="img/project_1.png"
alt="project 1 logo"
class="project-mini__logo"
/>
<a href="project_1.html" class="btn project-mini__btn"
>More</a
>
</div>
<!-- project 2 card -->
<div class="project-mini">
<h2 class="project-mini__title">
Value-based decision making
</h2>
<p class="project-mini__desc">
We seek to understand how the brain implements valuation
and decision making algorithms and how they interact
during learning.
</p>
<img
src="img/project_2.png"
alt="project 2 logo"
class="project-mini__logo"
/>
<a href="project_2.html" class="btn project-mini__btn"
>More</a
>
</div>
</aside>
</div>
<footer>
<div class="container container--footer">
<!-- twitter and github icons -->
<div class="social">
<a
href="https://github.com/compneuro-ncu"
class="social__link social__link--github"
>
<i class="social__icon fab fa-github"></i>
</a>
<a
href="https://twitter.com/karofinc"
class="social__link social__link--twitter"
>
<i class="social__icon fab fa-twitter"></i>
</a>
</div>
<!-- contact information -->
<div class="address">
<a href="https://www.umk.pl/en/" class="address__uni-link">
<img
src="img/ncu-logo.svg"
alt=""
class="address__uni-logo"
/>
</a>
<div class="address__group">
COMPUTATIONAL NEUROIMAGING TEAM<br />
Centre for Modern Interdisciplinary Technologies<br />
Nicolaus Copernicus University in Toruń<br />
Wileńska 4, 87-100 Toruń, Poland<br />
</div>
</div>
</div>
</footer>
</body>
</html>