remove duplicates in doc (#661)

README.md

@@ -13,23 +13,6 @@
 
 <!-- markdown-link-check-enable -->
 
-- [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)

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)
-  )