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

DOC: Add long description including background/significance #243

Merged
merged 1 commit into from
Oct 12, 2022
Merged
Show file tree
Hide file tree
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
44 changes: 44 additions & 0 deletions long_description.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
Magnetic resonance imaging (MRI) requires a set of preprocessing steps before
any statistical analysis. In an effort to standardize preprocessing,
we developed [fMRIPrep](https://fmriprep.org/en/stable/) (a preprocessing tool
for functional MRI, fMRI), and generalized its standardization approach to
other neuroimaging modalities ([NiPreps](https://www.nipreps.org/)). NiPreps
brings standardization and ease of use to the researcher, and effectively
limits the methodological variability within preprocessing. fMRIPrep is designed
to be used across wide ranges of populations; however it is designed for (and
evaluated with) human adult datasets. Infant MRI (i.e., 0-2 years) presents
unique challenges due to head size (e.g., reduced SNR and increased partial
voluming and rapid shifting in tissue contrast due to myelination. These and
other challenges require a more specialized workflow. *NiBabies*, an open-source
pipeline extending from fMRIPrep for infant structural and functional MRI
preprocessing, aims to address this need.

The workflow is built atop [Nipype](https://nipype.readthedocs.io) and encompases a large
set of tools from well-known neuroimaging packages, including
[FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/),
[ANTs](https://stnava.github.io/ANTs/),
[FreeSurfer](https://surfer.nmr.mgh.harvard.edu/),
[AFNI](https://afni.nimh.nih.gov/),
[Connectome Workbench](https://humanconnectome.org/software/connectome-workbench),
and [Nilearn](https://nilearn.github.io/).
This pipeline was designed to provide the best software implementation for each state of
preprocessing, and will be updated as newer and better neuroimaging software becomes
available.

*NiBabies* performs basic preprocessing steps (coregistration, normalization, unwarping,
segmentation, skullstripping etc.) providing outputs that can be
easily submitted to a variety of group level analyses, including task-based or resting-state
fMRI, graph theory measures, surface or volume-based statistics, etc.
*NiBabies* allows you to easily do the following:

* Take fMRI data from *unprocessed* (only reconstructed) to ready for analysis.
* Implement tools from different software packages.
* Achieve optimal data processing quality by using the best tools available.
* Generate preprocessing-assessment reports, with which the user can easily identify problems.
* Receive verbose output concerning the stage of preprocessing for each subject, including
meaningful errors.
* Automate and parallelize processing steps, which provides a significant speed-up from
typical linear, manual processing.

[Repository](https://github.com/nipreps/nibabies)
[Documentation](https://nibabies.readthedocs.io/en/stable/)
2 changes: 1 addition & 1 deletion setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ classifiers =
Programming Language :: Python :: 3.9
description = NeuroImaging Babies provides processing tools for magnetic resonance images of the brain in infants.
license = Apache License, 2.0
long_description = file:README.md
long_description = file:long_description.md
long_description_content_type = text/markdown; charset=UTF-8
project_urls =
Documentation=https://nibabies.readthedocs.io/en/latest/
Expand Down