From 276bc6a950062ce4afa968c952b969e2f943c35b Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Wed, 6 Dec 2023 18:47:15 +0100 Subject: [PATCH] remove duplicates in doc (#661) --- README.md | 70 ++++++------------ docs/source/general_information.md | 111 +---------------------------- 2 files changed, 23 insertions(+), 158 deletions(-) diff --git a/README.md b/README.md index f9621378..16cb5ece 100644 --- a/README.md +++ b/README.md @@ -13,23 +13,6 @@ -- [BIDS for MATLAB / Octave](#bids-for-matlab--octave) - - [Requirements](#requirements) - - [Installation](#installation) - - [Get the latest features](#get-the-latest-features) - - [Features](#features) - - [What this toolbox can do](#what-this-toolbox-can-do) - - [What this toolbox cannot do... yet](#what-this-toolbox-cannot-do-yet) - - [What will this toolbox most likely never do](#what-will-this-toolbox-most-likely-never-do) - - [Usage](#usage) - - [Demos](#demos) - - [Requirements](#requirements-1) - - [Reading and writing JSON files](#reading-and-writing-json-files) - - [Implementation](#implementation) - - [Get in touch](#get-in-touch) - - [Other tools (MATLAB only)](#other-tools-matlab-only) - - [Contributing](#contributing) - # BIDS for MATLAB / Octave This repository aims at centralising MATLAB/Octave tools to interact with @@ -40,12 +23,23 @@ For more information about BIDS, visit https://bids.neuroimaging.io/. See also [PyBIDS](https://github.com/bids-standard/pybids) for Python and the [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit). -## Requirements +## Installation + +### Requirements + +BIDS-MATLAB works with: + +- Octave 5.2.0 or newer +- MATLAB R2014a or newer + +We aim for compatibility with the latest stable release of Octave at any time. +Compatibility can sometimes also be achieved with older versions of Octave but +this is not guaranteed. For MacOS and Unix system, using `bids.copy_to_derivative` requires a version of gunzip >= 1.6. -## Installation +### Download or clone Download, unzip this repository and add its content to the MATLAB/Octave path. @@ -167,17 +161,6 @@ content = bids.util.jsondecode('/home/data/some_json_file.json'); There are demos and tutorials showing some of the features in the `demos` folder. -## Requirements - -BIDS-MATLAB works with: - -- Octave 5.2.0 or newer -- MATLAB R2014a or newer - -We aim for compatibility with the latest stable release of Octave at any time. -Compatibility can sometimes also be achieved with older versions of Octave but -this is not guaranteed. - ### Reading and writing JSON files Make sure to be familiar with the [JSON 101](https://bids-standard.github.io/stats-models/json_101.html). @@ -193,13 +176,6 @@ supported JSON library for your MATLAB or Octave. This can be any of: - [JSONio](https://github.com/gllmflndn/JSONio) for MATLAB or Octave - [SPM12](https://www.fil.ion.ucl.ac.uk/spm/software/spm12/) -## Implementation - -Starting point was `spm_BIDS.m` from [SPM12](https://github.com/spm/spm12) -([documentation](https://en.wikibooks.org/wiki/SPM/BIDS#BIDS_parser_and_queries)) -reformatted in a `+bids` package with dependencies to other SPM functions -removed. - ## Get in touch To contact us: @@ -212,17 +188,14 @@ on the brainhack mattermost ## Other tools (MATLAB only) -- [dicm2nii](https://github.com/xiangruili/dicm2nii): A DICOM to BIDS - converter -- [imtool3D_BIDS](https://github.com/tanguyduval/imtool3D_td): A 3D viewer for - BIDS directory -- [Brainstorm](https://github.com/brainstorm-tools/brainstorm3): Comprehensive - brain analysis toolbox (includes BIDS - [import and export](https://neuroimage.usc.edu/brainstorm/ExportBids) and - different examples dealing with BIDS datasets (e.g. - [group analysis from a MEG visual dataset](https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup), - [resting state analysis from OMEGA datasets](https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega#BIDS_specifications) - ) +- [dicm2nii](https://github.com/xiangruili/dicm2nii): A DICOM to BIDS converter +- [imtool3D_BIDS](https://github.com/tanguyduval/imtool3D_td): A 3D viewer for BIDS directory +- [Brainstorm](https://github.com/brainstorm-tools/brainstorm3): + Comprehensive brain analysis toolbox + (includes BIDS [import and export](https://neuroimage.usc.edu/brainstorm/ExportBids) and + different examples dealing with BIDS datasets + (e.g. [group analysis from a MEG visual dataset](https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup), + [resting state analysis from OMEGA datasets](https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega#BIDS_specifications)) ## How to cite To credit BIDS-Matlab in your work, please cite the [Zenodo archive](https://zenodo.org/record/5910584), @@ -239,7 +212,6 @@ doi = https://doi.org/10.5281/zenodo.3363985 } ``` - ## Contributing If you want to contribute make sure to check our [contributing guidelines](CONTRIBUTING.md) diff --git a/docs/source/general_information.md b/docs/source/general_information.md index 058a27bf..b56efe5a 100644 --- a/docs/source/general_information.md +++ b/docs/source/general_information.md @@ -12,93 +12,10 @@ on the brainhack mattermost and our [google group](https://groups.google.com/g/b See also [PyBIDS](https://github.com/bids-standard/pybids) for Python and the [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit). -## Installation +## Installation, Features -Download, unzip this repository and add its content to the MATLAB/Octave path. +Please see the [relevant sections of the README](https://github.com/bids-standard/bids-matlab) -```Matlab -unzip('https://github.com/bids-standard/bids-matlab/archive/main.zip'); -addpath('bids-matlab-main'); -``` - -Or clone it with git: - -```bash -git clone https://github.com/bids-standard/bids-matlab.git -``` - -and then add it to your MATLAB/Octave path. - -```Matlab -addpath('bids-matlab'); -``` - -### Get the latest features - -Stable versions should be fetched from a specific version tag. - -The latest features of bids-matlab that are in development are in our `main` -"branch". - -To access them you can either download the `main` branch from there: -https://github.com/bids-standard/bids-matlab/tree/main - -Or you can check it out the `main` branch after the adding this official -bids-matlab repository as a remote. - -``` -git add remote upstream https://github.com/bids-standard/bids-matlab.git -git checkout upstream/main -``` - -## Features - -### What this toolbox can do - -- read the layout of a BIDS dataset (see `bids.layout`), -- perform queries on that layout to get information about the subjects, - sessions, runs, modalities, metadata... contained within that dataset (see - `bids.query`), -- parse the layout of "BIDS-derivative compatible" datasets (like those - generated by fMRIprep), - -- create BIDS compatible filenames or folder structures for raw or derivatives - datasets (`bids.File`, `bids.util.mkdir`, - `bids.dataset_description`), -- do basic copying of files to help initialize a derivative dataset - to start a new analysis (`bids.copy_to_derivative`), - -- generate a human readable report of the content of BIDS data set containing - anatomical MRI, functional MRI, diffusion weighted imaging, field map data - (see `bids.report`) -- read and write JSON files (see `bids.util.jsondecode` and - `bids.util.jsonwrite`) provided that the right - [dependencies](#reading-and-writing-json-files) are installed, -- read and write TSV files (see `bids.util.tsvread` and `bids.util.tsvwrite`) - -- access and query the BIDS schema (bids.schema) - -The behavior of this toolbox assumes that it is interacting with a valid BIDS -dataset that should have been validated using -[BIDS-validator](https://bids-standard.github.io/bids-validator/). If the -Node.js version of the validator is -[installed on your computer](https://github.com/bids-standard/bids-validator#quickstart), -you can call it from the matlab prompt using `bids.validate`. Just be aware that -any unvalidated components may produce undefined behavior. Although, if you're -BIDS-y enough, the behavior may be predictable. - -### What this toolbox cannot do... yet - -- generate human readable reports of the content of BIDS data with EEG, MEG, - iEEG, physio and events data, -- deal with some of the incoming BIDS extensions (BIDS model...) - -### What will this toolbox most likely never do - -- act as a Matlab / Octave based BIDS-validator -- act as a BIDS converter -- implement reading / writing capabilities for the different modality-specific - data format that exist in BIDS (`.nii`, `.eeg`, `.ds`, `.fif`...) ## Usage @@ -123,16 +40,6 @@ A are available as a Jupyter Notebooks and scripts and can be run interactively via [Binder](https://mybinder.org/v2/gh/bids-standard/bids-matlab/main?urlpath=demos). -## Requirements - -BIDS-MATLAB works with: - -- Octave 5.2.0 or newer -- MATLAB R2014a or newer - -We aim for compatibility with the latest stable release of Octave at any time. -Compatibility can sometimes also be achieved with older versions of Octave but -this is not guaranteed. ### Reading and writing JSON files @@ -150,17 +57,3 @@ Starting point was `spm_BIDS.m` from [SPM12](https://github.com/spm/spm12) ([documentation](https://en.wikibooks.org/wiki/SPM/BIDS#BIDS_parser_and_queries)) reformatted in a `+bids` package with dependencies to other SPM functions removed. - -## Other tools (MATLAB only) - -- [dicm2nii](https://github.com/xiangruili/dicm2nii): A DICOM to BIDS - converter -- [imtool3D_BIDS](https://github.com/tanguyduval/imtool3D_td): A 3D viewer for - BIDS directory -- [Brainstorm](https://github.com/brainstorm-tools/brainstorm3): Comprehensive - brain analysis toolbox (includes BIDS - [import and export](https://neuroimage.usc.edu/brainstorm/ExportBids) and - different examples dealing with BIDS datasets (e.g. - [group analysis from a MEG visual dataset](https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup), - [resting state analysis from OMEGA datasets](https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega#BIDS_specifications) - )