Nicole Nogoy

[![Cameron
Craddock](http://gigasciencejournal.com/blog/wp-content/uploads/2016/03/Cameron-Craddock_400x400-300x300.png){.wp-image-1707
loading="lazy" decoding="async" width="250" height="250"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2016/03/Cameron-Craddock_400x400-300x300.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2016/03/Cameron-Craddock_400x400-150x150.png 150w, http://gigasciencejournal.com/blog/wp-content/uploads/2016/03/Cameron-Craddock_400x400-100x100.png 100w, http://gigasciencejournal.com/blog/wp-content/uploads/2016/03/Cameron-Craddock_400x400.png 400w"
sizes="(max-width: 250px) 100vw, 250px"}](http://gigasciencejournal.com/blog/wp-content/uploads/2016/03/Cameron-Craddock_400x400.png)

*In support of Brain Awareness Week, we have asked Cameron Craddock,
Director of the Computational NeuroImaging Lab, Nathan S. Kline
Institute for Psychiatric Research and Director of Imaging, Child Mind
Institute, to write a blog highlighting open science in neuroimaging,
and to announce our upcoming publication of the 2015 Brainhack
Proceedings and the Brainhack Thematic Series. BioMed Central are also
highlighting some of the amazing benefits of brain research and
showcasing the progress being made by researchers around to world.*

The principles of open science have permeated neuroimaging to the point
that nearly every software tool produced is free and open source and
most new neuroimaging datasets are earmarked for data sharing. As these
open science resources continue to blossom it is important to reflect on
the importance of community-based efforts to nurture these resources so
that they maintain their relevance well into the future. Here, I will
highlight just a few of the many different ways the community can make a
significant impact on open science by contributing their time and
effort:

#### Annotation and Curation of Literature

The scientific literature represents the collective knowledge of a
research community, but, can be notoriously difficult to index and even
harder to extract meaningful information from. Databasing efforts such
as [Brainmap](http://brainmap.org/) and
[BrainSpell](http://brainspell.org/) attempt to index the literature by
manually annotating publications in their databases with a variety of
tags that describe its nature. To enable meta-analyses, these databases
also store the brain areas implicated by each publication.
[Neurovault](http://neurovault.org/) takes this a step further by asking
authors to directly upload the statistical maps produced by their
various analyses. Other useful ways to contribute to literature curation
involve creating topic-specific literature collections in
[Mendeley](https://www.mendeley.com/) or
[Citeulike](http://www.citeulike.org/) to help make relevant
publications easier to find.

#### Data inspection, Preprocessing, and Manual Correction

There are a variety of large neuroimaging data-sharing repositories
available and each has made a gallant effort to organize its data.
Nonetheless, there remain many ways in which users of these repositories
can contribute their time to make them better. Every user of the raw
data from these repositories needs to manually inspect the data to
exclude poor quality images, preprocess the data to make it usable for
analyses, and potentially make manual corrections to fix preprocessing
errors.  If done well, each of these steps need only be done once, and
can be shared with all of the other users of the data. Additionally,
particularly time consuming corrections could be accomplished much
faster if performed by many. As one example, the [Preprocessed
Connectomes Project](http://preprocessed-connectomes-project.org) is
performing these tasks for the data shared through the [International
Neuroimaging Datasharing
Initiative](http://fcon_1000.projects.nitrc.org), but given the
widespread use of such data, further initiatives of this sort would be a
welcome contribution from the wider community.

#### Software Review, Testing, and Evaluation

Free and open source software tools are the backbone of neuroimaging and
there are many ways that the community can contribute to improving their
quality. Simply providing feedback on usability and bug reports are in
themselves invaluable contributions. Other important contributions
include: performing detailed code reviews, improving the build system,
setting up continuous integration testing, optimizing the code to work
more efficiently or use high performance computing, simplifying software
installation, etc... The
[Neurodebian](http://neuro.debian.net/) software repository and the
[testkraut](http://testkraut.readthedocs.org/en/latest/design.html) software
testing framework are two examples of projects that are improving the
usability and quality of neuroimaging software.

The lack of a system for providing scientific compensation for the
effort spent on these types of contributions is a major hurdle that
limits more widespread involvement. Although platforms have been created
for publications describing shared data and new software tools, nothing
currently exists for describing large-scale collaborative crowdsourcing
initiatives. For these reasons it is very important to acknowledge the
contributors of the open science repositories you benefit from in your
publications. [Zenodo](https://zenodo.org/) can help with this by
providing ISBNs and citable references for different versions of project
outputs, which would essentially enable to the author list to expand as
new contributors are engaged. The
[Duecredit](https://github.com/duecredit) project provides a means for
tracking the citations for the various software tools that are used in
performing an analysis, to help avoid leaving anyone out.

[![A22316_LG_BMC_BioSc_NN_GigaSc_Brainhack_widget\_#2](http://gigasciencejournal.com/blog/wp-content/uploads/2016/03/A22316_LG_BMC_BioSc_NN_GigaSc_Brainhack_widget_2-300x207.jpg){.wp-image-1708
.alignleft loading="lazy" decoding="async" width="275"
height="190"}](http://gigasciencejournal.com/blog/wp-content/uploads/2016/03/A22316_LG_BMC_BioSc_NN_GigaSc_Brainhack_widget_2.jpg)

#### Brainhack: Open Tools for Neuroscience -- Calling for Papers {#brainhack-open-tools-for-neuroscience-calling-for-papers style="text-align: justify;"}

In 2012, my colleagues in the Neuro Bureau and I started hosting
[Brainhack](http://brainhack.org) events to convene researchers from a
variety of backgrounds to work together in open collaboration. Many of
the projects performed during these events are contributions of effort
aimed to improve existing open science resources. We feel that
[*GigaScience*](http://Gigasciencejournal.com) is a natural partner for
Brainhack given their ethos of supporting openness and reproducibility
in science by publishing all research objects (open data, tools,
workflows and pipelines). And in partnership, we will be publishing
annual Brainhack Proceedings to provide attendees with a peer reviewed
publication outlet for reports on projects performed during Brainhack
events.

We plan for the 2015 Brainhack Proceedings to be out by the end of March
2016. We have also partnered with *GigaScience* to publish a Brainhack
Thematic series for full-length publications that describe projects in
neuroscience that embody the ethos of open science. Example topics
include open source software tools, data repositories, collaborative
projects, and other open science initiatives -- regardless of whether
they have roots at Brainhack events. I look forward to your contribution
to both of these publication venues and look forward to the opportunity
to collaborate with you at an upcoming Brainhack event.

Please join me in the upcoming [Brainhack](http://brainhack.org/)
events:

- [[26-30 June, 2016 ]{.aQJ}]{.aBn}[OHBM
  Hackathon](http://events.brainhack.org/OHBM2016/), Lausanne,
  Switzerland
- [[18-20 September, 2016 ]{.aQJ}]{.aBn}[Brainhack
  Vienna](http://events.brainhack.org/vienna/), Vienna, Austria
- 10-12 November, 2016 [Brainhack
  LA](http://events.brainhack.org/LA2016/), Los Angeles, USA

#### Acknowledgement

I would like to thank Daniel Margulies for his helpful comments that
helped to improve the quality of this blog.

------------------------------------------------------------------------

See what else we're doing in support of Brain Awareness Week
[here](http://www.biomedcentral.com/p-brainawarenessweek).

The post [Open Science Resources for Contributing to Brain Imaging
Research: A Guest Blog by Cameron
Craddock](http://gigasciencejournal.com/blog/open-science-resources-contributing-brain-imaging-research-guest-blog-cameron-craddock/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


<em>
 In support of Brain Awareness Week, we have asked Cameron Craddock, Director of the Computational NeuroImaging Lab, Nathan S. Kline Institute for Psychiatric Research and Director of Imaging, Child Mind Institute, to write a blog highlighting open science in neuroimaging, and to announce our upcoming publication of the 2015 Brainhack Proceedings and the Brainhack Thematic Series.
</em>

Publicaciones de Rogue Scholar

Open Science Resources for Contributing to Brain Imaging Research: A Guest Blog by Cameron Craddock