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DOC: Add long description including background/significance [skip ci]
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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. | ||
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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. | ||
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*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: | ||
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* 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. | ||
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[Repository](https://github.com/nipreps/nibabies) | ||
[Documentation](https://nibabies.readthedocs.io/en/stable/) |
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