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| 1 | +Magnetic resonance imaging (MRI) requires a set of preprocessing steps before |
| 2 | +any statistical analysis. In an effort to standardize preprocessing, |
| 3 | +we developed [fMRIPrep](https://fmriprep.org/en/stable/) (a preprocessing tool |
| 4 | +for functional MRI, fMRI), and generalized its standardization approach to |
| 5 | +other neuroimaging modalities ([NiPreps](https://www.nipreps.org/)). NiPreps |
| 6 | +brings standardization and ease of use to the researcher, and effectively |
| 7 | +limits the methodological variability within preprocessing. fMRIPrep is designed |
| 8 | +to be used across wide ranges of populations; however it is designed for (and |
| 9 | +evaluated with) human adult datasets. Infant MRI (i.e., 0-2 years) presents |
| 10 | +unique challenges due to head size (e.g., reduced SNR and increased partial |
| 11 | +voluming and rapid shifting in tissue contrast due to myelination. These and |
| 12 | +other challenges require a more specialized workflow. *NiBabies*, an open-source |
| 13 | +pipeline extending from fMRIPrep for infant structural and functional MRI |
| 14 | +preprocessing, aims to address this need. |
| 15 | + |
| 16 | +The workflow is built atop [Nipype](https://nipype.readthedocs.io) and encompases a large |
| 17 | +set of tools from well-known neuroimaging packages, including |
| 18 | +[FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), |
| 19 | +[ANTs](https://stnava.github.io/ANTs/), |
| 20 | +[FreeSurfer](https://surfer.nmr.mgh.harvard.edu/), |
| 21 | +[AFNI](https://afni.nimh.nih.gov/), |
| 22 | +[Connectome Workbench](https://humanconnectome.org/software/connectome-workbench), |
| 23 | +and [Nilearn](https://nilearn.github.io/). |
| 24 | +This pipeline was designed to provide the best software implementation for each state of |
| 25 | +preprocessing, and will be updated as newer and better neuroimaging software becomes |
| 26 | +available. |
| 27 | + |
| 28 | +*NiBabies* performs basic preprocessing steps (coregistration, normalization, unwarping, |
| 29 | +segmentation, skullstripping etc.) providing outputs that can be |
| 30 | +easily submitted to a variety of group level analyses, including task-based or resting-state |
| 31 | +fMRI, graph theory measures, surface or volume-based statistics, etc. |
| 32 | +*NiBabies* allows you to easily do the following: |
| 33 | + |
| 34 | + * Take fMRI data from *unprocessed* (only reconstructed) to ready for analysis. |
| 35 | + * Implement tools from different software packages. |
| 36 | + * Achieve optimal data processing quality by using the best tools available. |
| 37 | + * Generate preprocessing-assessment reports, with which the user can easily identify problems. |
| 38 | + * Receive verbose output concerning the stage of preprocessing for each subject, including |
| 39 | + meaningful errors. |
| 40 | + * Automate and parallelize processing steps, which provides a significant speed-up from |
| 41 | + typical linear, manual processing. |
| 42 | + |
| 43 | +[Repository](https://github.com/nipreps/nibabies) |
| 44 | +[Documentation](https://nibabies.readthedocs.io/en/stable/) |
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