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*NiBabies* is an extension of [fMRIPrep](https://fmriprep.org/en/stable/) designed and tested for infants 0-2 years old. *NiBabies* offers structural and functional MRI preprocessing.
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*NiBabies* is an open-source software pipeline designed to process anatomical and functional magnetic resonance imaging data.
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A member of the [NeuroImaging PREProcessing toolS (NiPreps)](https://www.nipreps.org/) family, *NiBabies* is designed and optimized for human infants between 0-2 years old.
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---
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## Getting Started
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Before using *NiBabies*, you will need to have your MRI data formatted in [BIDS](https://bids.neuroimaging.io/).
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This helps the software locate the available data, and optimize the workflow accordingly.
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### Installing NiBabies
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Given its extensive dependencies, the easiest way to get up and running with *NiBabies* is by using the available [Docker](https://hub.docker.com/r/nipreps/nibabies/tags?page=1&ordering=last_updated) containers.
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Images are all tagged with the release number, which must be specified in order to pull the images. For example, if you wanted to pull version `21.0.0rc1`, you would use the following command.
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```
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# Docker
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docker pull nipreps/nibabies:21.0.0rc1
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```
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However, if you would prefer to install this tool natively, you can refer the [Dockerfile](./Dockerfile) as a guide for all the dependencies.
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---
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## Usage
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*NiBabies* follow the [BIDS App Specifications](http://bids-apps.neuroimaging.io/about/), meaning you only need to provide three positional arguments:
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-**bids_dir** - the root folder of a BIDS valid dataset.
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-**output_dir** - folder to store outputs and reports.
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-**level** - processing stage to be run, currently can only be `participant`.
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However, as infant brains can vastly differ depending on age, providing the following arguments is highly recommended:
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-**--age-months** - participant age in months
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> **_NOTE:_** This is required when using Infant FreeSurfer
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-**--segmentation-atlases-dir** - directory containing pre-labeled segmentations to use for Joint Label Fusion.
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> **_NOTE:_** The segmentation directory should consist of one or more template directories containing:
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> - A segmented and labelled NIfTI that includes `Segmentation` in the filename.
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> - A brainmasked T1w NIfTI that includes `T1w` in the filename.
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To view all options, see the [Command-Line Arguments](https://nibabies.readthedocs.io/usage.html#command-line-arguments) section of the documentation.
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---
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## Running with ``nibabies-wrapper``
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The ``nibabies-wrapper`` is a lightweight Python 2/3 wrapper for running *NiBabies* via Docker and Singularity.
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It will generate a Docker/Singularity command line for you, print it out for reporting purposes, and then execute it without further action needed, e.g.:
Note that the `-i` flag is required when using Singularity, and should be the path to the already built Singularity image file.
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The ``nibabies-wrapper`` accepts all of the [available options for NiBabies](#usage), automatically translating local files and directories into mount points.
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---
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## Outputs
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TODO - Refer to [fMRIPrep's outputs](https://fmriprep.org/en/20.2.1/outputs.html) for now.
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For comprehensive information on *NiBabies*, including installation and usage, visit [our documentation](https://nibabies.readthedocs.io/en/latest).
Given its extensive dependencies, the easiest way to get up and running with *NiBabies* is by using a container service, such as [Docker](https://www.docker.com/get-started) or [Singularity](https://sylabs.io/singularity/).
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### Working with Docker
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Images are hosted on our [Docker Hub](https://hub.docker.com/r/nipreps/nibabies).
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To pull an image, the specific version tag must be specified in order to pull the images.
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For example, if you want to pull version `21.0.0`, you would use the following command.
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```
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$ docker pull nipreps/nibabies:21.0.0
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```
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There are also a few keyword tags, `latest` and `unstable`, that serve as special pointers.
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`latest` points to the latest release (excluding any betas or release candidates).
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`unstable` points to the most recent developmental change, and should only be used to test new features or fixes.
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### Working with Singularity
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The easiest way to create a Singularity image is to build from the [Docker](#working-with-docker) images hosted online.
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For example, if you want to build version `21.0.0`, you would use the following command.
The `nibabies-wrapper` is a lightweight Python tool to facilitate running `nibabies` within a container service.
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To install or upgrade to the current release:
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```
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$ pip install --update nibabies-wrapper
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```
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For further details, see [](usage.md#using-the-nibabies-wrapper).
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## Bare-metal Installation
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If you would prefer to install this tool natively, you can refer the [Dockerfile](https://github.com/nipreps/nibabies/blob/master/Dockerfile) as a guide for all the dependencies.
*NiBabies* uses FreeSurfer tools, which require a license to run.
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To obtain a FreeSurfer license, simply register for free at https://surfer.nmr.mgh.harvard.edu/registration.html.
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FreeSurfer will search for a license key file first using the `$FS_LICENSE` environment variable and then in the default path to the license key file (`$FREESURFER_HOME`/license.txt). If `$FS_LICENSE` is set, the [`nibabies-wrapper`](#using-the-nibabies-wrapper) will automatically handle setting the license within the container.
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Otherwise, you will need to use the `--fs-license-file` flag to ensure the license is available.
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## Command-Line Arguments
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```{argparse}
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:ref: nibabies.cli.parser._build_parser
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:prog: nibabies
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:nodefault:
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:nodefaultconst:
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```
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The command-line interface of the docker wrapper
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## More information on command-line arguments
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At minimum, the following *positional* arguments are required.
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-**`bids_dir`** - the root folder of a BIDS valid dataset.
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-**`output_dir`** - folder to store outputs and reports.
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-**`level`** - processing stage to be run, currently can only be `participant`.
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However, as infant brains can vastly differ depending on age, providing the following arguments is highly recommended:
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-**`--age-months`** - participant age in months
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:::{admonition} Warning
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:class: warning
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This is required if FreeSurfer is not disabled (`--fs-no-reconall`)
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:::
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-**`--participant-id`** - participant ID
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:::{admonition} Tip
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:class: tip
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This is recommended when using `--age-months` if age varies across participants.
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:::
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-**`--segmentation-atlases-dir`** - directory containing pre-labeled segmentations to use for Joint Label Fusion.
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:::{admonition} Tip
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:class: tip
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The segmentation directory layout should consist of one or more template directories containing:
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* A segmented and labeled NIfTI that includes `Segmentation` in the filename.
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* A brainmasked T1w NIfTI that includes `T1w` in the filename.
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:::
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## Using the nibabies wrapper
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The wrapper will generate a Docker or Singularity command line for you, print it out for reporting purposes, and then execute it without further action needed.
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For installation instructions, please see [](installation.md#installing-the-nibabies-wrapper)
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