From 39ea7b8e78233fdc821d6584a010aa02dbd8488a Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 22 Jun 2021 13:45:23 -0400 Subject: [PATCH 1/5] DOC: Add functional image to README --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 40da2865..2b63f4b2 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,7 @@

nibabies-anat + nibabies-func

*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. From 65702c387e749250c84d564cea8f5f38f9c35c22 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 22 Jun 2021 13:57:05 -0400 Subject: [PATCH 2/5] DOC: Add wrapper usage --- README.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/README.md b/README.md index 2b63f4b2..90234990 100644 --- a/README.md +++ b/README.md @@ -317,6 +317,27 @@ 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 +``` + ### Outputs TODO - Refer to [fMRIPrep's outputs](https://fmriprep.org/en/20.2.1/outputs.html) for now. From f00167c2fbbaee08b4036bfd2eb6d170bf9fe938 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 22 Jun 2021 14:03:44 -0400 Subject: [PATCH 3/5] DOC: Image formatting --- README.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 90234990..bab21840 100644 --- a/README.md +++ b/README.md @@ -3,11 +3,9 @@ ![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 - nibabies-func -

+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. From 122d4e67b3f4525e118168034659d11f233d7e06 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 22 Jun 2021 14:09:15 -0400 Subject: [PATCH 4/5] DOC: Clarify available options --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index bab21840..d72cb4a2 100644 --- a/README.md +++ b/README.md @@ -44,8 +44,10 @@ 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] @@ -336,6 +338,8 @@ 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. From 236544b979b4e59d1fb86577da0275c19784fe1e Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 22 Jun 2021 14:12:08 -0400 Subject: [PATCH 5/5] DOC: Visually separate header sections --- README.md | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index d72cb4a2..0d5654b3 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,8 @@ Anatomical | Functional *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. @@ -24,6 +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 @@ -317,8 +319,9 @@ NiBabies specific options:
+--- -#### Running with ``nibabies-wrapper`` +### 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.: @@ -340,6 +343,8 @@ RUNNING: singularity run --cleanenv -B /path/to/data:/data:ro \ 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.