From 41ea1a90934ef7074c40591758c769541f0590ce Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 25 Aug 2023 07:46:13 -0400 Subject: [PATCH] [ENH] organize list of tools (#338) * list tools * liquify rendering --- _data/converters.yml | 2 +- _data/tools.yml | 147 ++++++++++++++++++++++++++++++++++++++ _includes/list_tools.html | 9 +++ _pages/benefits.md | 27 +------ 4 files changed, 158 insertions(+), 27 deletions(-) create mode 100644 _data/tools.yml create mode 100644 _includes/list_tools.html diff --git a/_data/converters.yml b/_data/converters.yml index e8dace04..fb3df708 100644 --- a/_data/converters.yml +++ b/_data/converters.yml @@ -307,7 +307,7 @@ GUI: false - name: BIDSconvertR - url: https://github.com/wulms/bidsconvertr + url: https://github.com/bidsconvertr/bidsconvertr comment: | The BIDSconvertR R package provides a user-friendly workflow with graphical user interfaces. It consists of the following steps: diff --git a/_data/tools.yml b/_data/tools.yml new file mode 100644 index 00000000..19be03c9 --- /dev/null +++ b/_data/tools.yml @@ -0,0 +1,147 @@ +# - name: +# url: +# documentation: +# language: +# - +# description: +# distribution: +# - name: pypi +# url: +# - name: dockerhub +# url: + +- name: babs + url: https://github.com/PennLINC/babs + documentation: https://pennlinc-babs.readthedocs.io/ + language: + - Python + description: BIDS App Bootstrap (BABS) is a reproducible, generalizable, and scalable Python package for BIDS App analysis of large datasets. It uses DataLad and adopts FAIRly big framework. + distribution: + - name: pypi + url: https://pypi.org/project/babs/ + +- name: BIDSHandler + url: https://github.com/Macquarie-MEG-Research/BIDSHandler + language: + - Python + description: Python module allowing complete manipulation of BIDS data + +- name: bids-cfood + url: https://gitlab.indiscale.com/caosdb/src/crawler-cfoods/bids-cfood + language: + - Python + description: a module to handle BIDS dataset for the caosDB data crawler + +- name: bids2cite + url: https://github.com/Remi-Gau/bids2cite + language: + - Python + description: package to interactively update `dataset_description.json` and generate citation files (for example `datacite.yml`) for BIDS datasets. + +- name: bids-matlab + url: https://github.com/bids-standard/bids-matlab + language: + - MATLAB + - Octave + description: MATLAB/Octave tools to interact with datasets conforming to the BIDS format + +- name: BIDS-pydantic + url: https://github.com/gold-standard-phantoms/bids-pydantic + language: + - Python + description: "Pulls a specified version of the BIDS schema and creates corresponding Pydantic models, which will provide BIDS data validation using Python type annotations. See also [BIDS-pydantic-models](https://pypi.org/project/BIDS-pydantic-models/)." + distribution: + - name: pypi + url: https://pypi.org/project/BIDS-pydantic/ + +- name: bidser + url: https://github.com/bbuchsbaum/bidser + documentation: https://bbuchsbaum.github.io/bidser/ + language: + - R + description: Working with Brain Imaging Data Structure in R + +- name: Brainstorm + url: http://neuroimage.usc.edu/brainstorm/ + language: + - MATLAB + description: MEG/EEG analysis package + +- name: clpipe + url: https://github.com/cohenlabUNC/clpipe + documentation: https://clpipe.readthedocs.io/en/latest/index.html + language: + - Python + description: streamlined processing pipeline for MRI data centered around BIDS + +- name: cuBIDS + url: https://github.com/pennlinc/cubids + documentation: https://cubids.readthedocs.io/en/latest/ + language: + - Python + description: a Python package designed to facilitate reproducible curation of neuroimaging BIDS datasets + distribution: + - name: pypi + url: https://pypi.org/project/cubids/ + +- name: GUI dataset description generator + url: https://github.com/tolik-g/BIDS + documentation: + language: + - Python + description: GUI form that generates `dataset_description.json` + +- name: Lead-DBS + url: https://www.lead-dbs.org/ + language: + - MATLAB + description: A toolbox facilitating Deep Brain Stimulation electrode reconstructions and computer simulations supports BIDS conversion and ingestion of BIDS datasets. + +- name: mne-bids + url: https://github.com/mne-tools/mne-bids + documentation: https://mne.tools/mne-bids/stable/index.html + language: + - Python + description: collection of tools for converting magnetoencephalography (MEG) data into BIDS format, as well as some helper functions for creating the folders and metadata needed for a BIDS dataset. + +- name: OpenNeuro + url: http://openneuro.org + description: A free and open platform for validating and sharing BIDS-compliant data. + +- name: PRFmodel + url: https://github.com/vistalab/PRFmodel + documentation: https://github.com/vistalab/PRFmodel/wiki + description: a set of tools to fit population receptive field models to BIDS datasets + distribution: + - name: dockerhub + url: + - https://hub.docker.com/r/garikoitz/prfsynth + - https://hub.docker.com/r/garikoitz/prfanalyze-vista + - https://hub.docker.com/r/garikoitz/prfanalyze-afni + - https://hub.docker.com/r/garikoitz/prfanalyze-aprf + - https://hub.docker.com/r/garikoitz/prfanalyze-popeye + - https://hub.docker.com/r/garikoitz/prfreport + +- name: PyBIDS + url: https://github.com/bids-standard/pybids + documentation: + language: + - Python + description: Python package to quickly parse / search the components of a BIDS dataset. It also contains functionality for running analyses on your data. + distribution: + - name: pypi + url: https://pypi.org/project/pybids/ + +- name: rbids + url: https://github.com/mathesong/rbids + language: + - R + description: aims to make BIDS datasets more easily accessible for packages written in R + +- name: spm_2_bids + url: https://github.com/cpp-lln-lab/spm_2_bids + documentation: https://spm-2-bids.readthedocs.io/en/latest/ + language: + - MATLAB + - Octave + description: a tool convert SPM preprocessed output to BIDS derivatives (trying to follow [BEP12](https://bids.neuroimaging.io/bep012)) diff --git a/_includes/list_tools.html b/_includes/list_tools.html new file mode 100644 index 00000000..1cabc724 --- /dev/null +++ b/_includes/list_tools.html @@ -0,0 +1,9 @@ +
+ +
diff --git a/_pages/benefits.md b/_pages/benefits.md index 7abc28e2..9008f900 100644 --- a/_pages/benefits.md +++ b/_pages/benefits.md @@ -30,29 +30,4 @@ A description of how to build containerized apps supporting BIDS inputs can be f ## Other Tools -- [BIDSHandler](https://github.com/Macquarie-MEG-Research/BIDSHandler){:target="_blank"} (Python module allowing complete manipulation of BIDS data) -- [bids-cfood](https://gitlab.indiscale.com/caosdb/src/crawler-cfoods/bids-cfood) - a module to handle BIDS dataset for the caosDB data crawler. -- [bids2cite](https://github.com/Remi-Gau/bids2cite){:target="_blank"} a python package - to interactively update `dataset_description.json` and generate citation files (for example `datacite.yml`) for BIDS datasets. -- [bids-matlab](https://github.com/bids-standard/bids-matlab){:target="_blank"} - (MATLAB/Octave tools to interact with datasets conforming to the BIDS format) -- [BIDS-pydantic](https://pypi.org/project/BIDS-pydantic/) pulls a specified version of the BIDS schema - and creates corresponding Pydantic models, which will provide BIDS data - validation using Python type annotations (see also [BIDS-pydantic-models](https://pypi.org/project/BIDS-pydantic-models/)). -- [Brainstorm](http://neuroimage.usc.edu/brainstorm/){:target="_blank"} (MEG/EEG analysis package) -- [clpipe](https://clpipe.readthedocs.io/en/latest/index.html){:target="_blank"} - streamlined processing pipeline for MRI data centered around BIDS. -- [cuBIDS](https://pypi.org/project/cubids/){:target="_blank"} - a Python package designed to facilitate reproducible curation of neuroimaging BIDS datasets. -- [GUI dataset description generator](https://github.com/tolik-g/BIDS){:target="_blank"} - (GUI form that generates dataset_description.json) -- [Lead-DBS](https://www.lead-dbs.org/) A toolbox facilitating Deep Brain Stimulation electrode reconstructions - and computer simulations supports BIDS conversion and ingestion of BIDS datasets. -- [OpenNeuro](http://openneuro.org){:target="_blank"} (repository) -- [PRFmodel](https://github.com/vistalab/PRFmodel){:target="_blank"} a set of tools - to fit population receptive field models to BIDS datasets. -- [PyBIDS](https://github.com/bids-standard/pybids){:target="_blank"} (Python module to harmonize access and manipulation) -- [rbids](https://github.com/mathesong/rbids) aims to make BIDS datasets more easily accessible for packages written in R. -- [spm_2_bids](https://github.com/cpp-lln-lab/spm_2_bids){:target="_blank"} a tool convert SPM preprocessed output - to BIDS derivatives (trying to follow [BEP12](https://bids.neuroimaging.io/bep012){:target="_blank"}) +{% include list_tools.html tools=site.data.tools %}