diff --git a/README.md b/README.md index 40da2865..0d5654b3 100644 --- a/README.md +++ b/README.md @@ -3,14 +3,14 @@ ![nibabies](https://github.com/nipreps/nibabies/actions/workflows/pytest.yml/badge.svg) [![DOI](https://zenodo.org/badge/264223087.svg)](https://zenodo.org/badge/latestdoi/264223087) - -

- nibabies-anat -

+Anatomical | Functional +---------- | ---------- +![nibabies-anat](./docs/_static/nibabies_anat.png) | ![nibabies-func](./docs/_static/nibabies_func.png) *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. ----- +--- + ### Requirements 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/mgxd/nibabies/tags?page=1&ordering=last_updated) or [Singularity](https://cloud.sylabs.io/library/mathiasg/default/nibabies) containers. @@ -25,6 +25,7 @@ singularity pull library://mathiasg/default/nibabies:0.1.0 If you insist on installing this tool locally, you can use the [Dockerfile](./Dockerfile) as a guide. +--- ### Usage @@ -45,8 +46,10 @@ However, as infant brains can vastly differ depending on age, providing the foll > - A segmented and labelled NIfTI that includes `Segmentation` in the filename. > - A brainmasked T1w NIfTI that includes `T1w` in the filename. + +##### Extensive Usage
-Extensive argument list +Click to view all options ``` usage: nibabies [-h] [--version] [--skip_bids_validation] @@ -316,6 +319,32 @@ NiBabies specific options:
+--- + +### Running with ``nibabies-wrapper`` + +The ``nibabies-wrapper`` is a lightweight Python 2/3 wrapper for running *NiBabies* via Docker and Singularity. +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.: + + +##### Docker +``` +$ nibabies-wrapper docker /path/to/data /path/to/output participant --age-months 12 +RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.6 -it -v /path/to/data:/data:ro \ +-v /path/to/output:/out nipreps/nibabies:0.1.1 /data /out participant --age-months 12 +``` + +##### Singularity +``` +$ nibabies-wrapper singularity /path/to/data /path/to/output participant --age-months 12 -i nibabies-0.1.1.sif +RUNNING: singularity run --cleanenv -B /path/to/data:/data:ro \ +-B /path/to/output:/out nibabies-0.1.1.sif /data /out participant --age-months 12 +``` + +The ``nibabies-wrapper`` accepts all of the [available options for NiBabies](#extensive-usage), automatically translating local files and directories into mount points. + +--- + ### Outputs TODO - Refer to [fMRIPrep's outputs](https://fmriprep.org/en/20.2.1/outputs.html) for now.