Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix typos, links #15

Merged
merged 1 commit into from
Aug 2, 2024
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 9 additions & 8 deletions docs/introduction/ecosystem.md
Original file line number Diff line number Diff line change
Expand Up @@ -20,34 +20,34 @@ large scale meta-analysis to provide new insights into the literature, overcomin
with sheer scale. With regular updates, Neurosynth was able to keep up with the growth of the literature.
The database was released with a permissive license, and accompanied by a Python package to manipulate and analyze it.

Although this approach was surprsingly successful, there were several major limitations to Neurosynth 1.0:
Although this approach was surprisingly successful, there were several major limitations to Neurosynth 1.0:

* Meta-analyses were limited by **concepts that can be inferred from large scale text mining** (i.e. frequency of terms in the text).
Although these features proved to be surprsingly useful for well-powered and broad cognitive constructs (e.g. 'emotion'), Neurosynth was not able
Although these features proved to be surprisingly useful for well-powered and broad cognitive constructs (e.g. 'emotion'), Neurosynth was not able
to capture the fine-grained details of the neuroimaging literature, or allow users to define their own grouping of studies.

* The database is not curated, and therefore contains many **inaccuracies and incomplete** data at both the study and coordinate level.
Aside from obvious extraction erors, automated coordinate extraction lacks the ability to determine critical information, such as whether the activation is positive or negative.
Aside from obvious extraction errors, automated coordinate extraction lacks the ability to determine critical information, such as whether the activation is positive or negative.
In addition, it's not possible to segregate the coordinates into distinct contrast, conditions, or studies without manual curation.

* Coordinate-based analyses are inherently **inferior to image-based** meta-analysis, which is becoming increasingly possible with sharing of unthresholded statisical maps in repositories like [NeuroVault][].
* Coordinate-based analyses are inherently **inferior to image-based** meta-analysis, which is becoming increasingly possible with sharing of unthresholded statistical maps in repositories like [NeuroVault][].

_Neurosynth Compose_ aims to address these limitations:

* Provides a web-based platform for meta-analytic neuroimaging research, allowing users to **curate studies**, and **specify meta-analytic models**.

* **Flexible and easy to use**, allowing users to perform both large-scale **exploratory** meta-analyses, as well as **targeted, hypothesis-driven** meta-analyses that conform to stringent standards such as the [PRISMA][https://prisma-statement.org] statement.
* **Flexible and easy to use**, allowing users to perform both large-scale **exploratory** meta-analyses, as well as **targeted, hypothesis-driven** meta-analyses that conform to stringent standards such as the [PRISMA][] statement.

* Allows users to perfom **image-based meta-analysis** using unthresholded images from NeuroVault (in progress).

* Quick, reproducible and transparent **sharing of results**.

* Incentivizes **collaborative curation** of neuroimaging studies in a accesible **centralized repository** (NeuroStore, see below).
* Incentivizes **collaborative curation** of neuroimaging studies in a accessible **centralized repository** (NeuroStore, see below).


## NeuroStore

NeuroStore is the centralized repository for neuroimaging data amenable to meta-analysis, including coordinates, images, and metadata.
[NeuroStore][] is the centralized repository for neuroimaging data amenable to meta-analysis, including coordinates, images, and metadata.
NeuroStore serves as the data backend for Neurosynth Compose, but is also designed to be a standalone interoperable resource for the neuroimaging community.

NeuroStore ingests data from a number of sources, including NeuroVault, NeuroQuery, and Neurosynth (ACE), and provides a unified API for querying the database.
Expand Down Expand Up @@ -79,7 +79,7 @@ NIMADS is used as a common, interoperable format by NeuroStore, pyNIMADS, and Ni
[NeuroQuery][] is a web service, Python library, and coordinate database built for large-scale, predictive meta-analysis.
Predictive meta-analysis generates non-statistical brain maps from text, using a database of coordinates and associated texts.

The [NeuroQuery dataset][] is accurate and maintainble than the existing Neurosynth 1.0 database,
The [NeuroQuery dataset][] is accurate and maintainable than the existing Neurosynth 1.0 database,
this new database will effectively replace the old one within the meta-analytic ecosystem.
NiMARE can ingest the NeuroQuery database and convert it automatically to a NiMARE Dataset object for analysis.
Additionally, the NeuroQuery database will feed directly into NeuroStore as a source of coordinates.
Expand Down Expand Up @@ -119,6 +119,7 @@ it is planned that NeuroVault will focus exclusively on image storage and sharin
[Nistats]: https://nistats.github.io/
[OpenNeuro]: https://openneuro.org
[peaks2maps]: https://doi.org/10.7490/f1000research.1116395.1
[PRISMA]: https://prisma-statement.org
[PyMARE]: https://pymare.readthedocs.io/en/latest/
[scikit-learn]: https://scikit-learn.org/stable/developers/index.html
[Sleuth]: http://www.brainmap.org/software.html#Sleuth
Expand Down
Loading