[DOC] Fix some broken links in docs

docs/BIDS.md

@@ -3,11 +3,10 @@
 
 ## Introduction
 
-[**BIDS**](http://bids.neuroimaging.io/) (Brain Imaging Data Structure) is the standard adopted for the organisation
- of the datasets used by Clinica pipelines through the command line.
- BIDS provides a unified structure for organising and describing neuroimaging and behavioural data.
- The use of a standard like BIDS makes easier developing and distributing code that uses neuroimaging datasets.
- For this reason, when using Clinica pipelines from the command line, the input format of the dataset is required to be BIDS-compliant.
+[**BIDS**](http://bids.neuroimaging.io/) (Brain Imaging Data Structure) is the standard adopted for the organisation of the datasets used by Clinica pipelines through the command line.
+[BIDS](http://bids.neuroimaging.io/) provides a unified structure for organising and describing neuroimaging and behavioural data.
+The use of a standard like [BIDS](http://bids.neuroimaging.io/) makes easier developing and distributing code that uses neuroimaging datasets.
+For this reason, when using Clinica pipelines from the command line, the input format of the dataset is required to be [BIDS](http://bids.neuroimaging.io/)-compliant.
 
 ## An overview of the BIDS structure
 
@@ -68,17 +67,21 @@ BIDS_Dataset/
 
 [bids-validator](https://github.com/bids-standard/bids-validator) can be run to ensure that a dataset is BIDS-compliant.
 
-Clinica provides tools to curate several publicly available neuroimaging datasets and convert them to BIDS. Datasets
-currently supported are:
+Clinica provides tools to curate several publicly available neuroimaging datasets and convert them to [BIDS](http://bids.neuroimaging.io/).
+
+Datasets currently supported are:
 
 - [ADNI](../Converters/ADNI2BIDS/)
 - [AIBL](../Converters/AIBL2BIDS/)
+- [GENFI](../Converters/GENFItoBIDS/)
+- [HABS](../Converters/HABS2BIDS/)
 - [NIFD](../Converters/NIFD2BIDS/)
 - [OASIS](../Converters/OASIS2BIDS/)
 - [OASIS-3](../Converters/OASIS3TOBIDS/)
+- [UKB](../Converters/UKBtoBIDS/)
 
 We decided to ignore several warnings and errors detected by the validator.
-These are listed in the `.bids-validator-config.json` and `.bidsignore` files at the root of each BIDS folder.
+These are listed in the `.bids-validator-config.json` and `.bidsignore` files at the root of each [BIDS](http://bids.neuroimaging.io/) folder.
 These files are automatically generated by Clinica converters to ignore the following issues:
 
 - Won't fix errors:

docs/Installation.md

@@ -10,8 +10,9 @@ if you encounter any issues.
 ## Prepare your Python environment
 
 You will need a Python environment to run Clinica.
+
 We advise you to use [Miniconda](https://docs.conda.io/en/latest/miniconda.html).
-Miniconda allows you to install, run, and update Python packages and their dependencies.
+[Miniconda](https://docs.conda.io/en/latest/miniconda.html) allows you to install, run, and update Python packages and their dependencies.
 It can also create environments to isolate your libraries.
 To install Miniconda, open a new terminal and type the following commands:
 
@@ -29,18 +30,18 @@ curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o /
 bash /tmp/miniconda-installer.sh
 ```
 
-Miniconda will ask you where to install it.
+[Miniconda](https://docs.conda.io/en/latest/miniconda.html) will ask you where to install it.
 Do not forget to copy the `export PATH` given at the end of the installation.
 If everything went fine, open a new terminal and type `conda info`, it will verify if
-Conda is installed, check the version and show your Miniconda path.
+Conda is installed, check the version and show your [Miniconda](https://docs.conda.io/en/latest/miniconda.html) path.
 
 ## Install Clinica
 
 The latest release of Clinica can be installed by using the conventional
 [PyPI package manager](https://pypi.org/project/clinica/) as follows:
 
 ```shell
-conda create --name clinicaEnv python=3.8
+conda create --name clinicaEnv python=3.10
 conda activate clinicaEnv
 pip install clinica
 ```
@@ -56,8 +57,7 @@ pip install clinica
 Depending on the pipeline that you want to use, you need to install
 **pipeline-specific interfaces**.
 Not all the dependencies are necessary to run Clinica.
-Please refer to [this section](../Third-party) to determine which third-party
-libraries you need to install.
+Please refer to [this section](../Third-party) to determine which third-party libraries you need to install.
 
 ## Shell completion (optional)
 
@@ -130,9 +130,8 @@ conda deactivate
 
 This section is intended for users who plan to contribute to Clinica or test the current development version.
 
-Clinica uses [Poetry](https://python-poetry.org) to manage its development environment. Please follow
-these [installation instructions](https://python-poetry.org/docs/#installation) and verify the `poetry` command is
-correctly setup.
+Clinica uses [Poetry](https://python-poetry.org) to manage its development environment.
+Please follow these [installation instructions](https://python-poetry.org/docs/#installation) and verify the `poetry` command is correctly setup.
 
 Clone the development branch of Clinica:
 

docs/InteractingWithClinica.md

@@ -9,8 +9,8 @@ The easiest way to use Clinica is to have your data organized using the [BIDS st
 If your dataset does not follow this standard, you will need to convert it:
 
 - If your data are in DICOM format, you can use one of the converters referenced on the [BIDS website](https://bids.neuroimaging.io/benefits.html#converters).
-- Otherwise, Clinica includes converters for public datasets such as [ADNI](http://adni.loni.usc.edu/), [AIBL](https://aibl.csiro.au), [NIFD](http://4rtni-ftldni.ini.usc.edu/) and [OASIS](http://www.oasis-brains.org).
-See [here](../DatabasesToBIDS) for more details.
+- Otherwise, Clinica includes converters for public datasets such as [ADNI](http://adni.loni.usc.edu/), [AIBL](https://aibl.csiro.au), [NIFD](http://4rtni-ftldni.ini.usc.edu/), [OASIS](http://www.oasis-brains.org), [UK Biobank](https://www.ukbiobank.ac.uk/), and [GENFI](https://www.genfi.org).
+See [here](../Converters/ADNI2BIDS) for more details.
 
 !!! note "Regarding cross-sectional BIDS datasets"
     If you run Clinica with a dataset containing no timepoints e.g.:
@@ -38,7 +38,7 @@ See [here](../DatabasesToBIDS) for more details.
     ```
 
 !!! tip
-     If you need to create BIDS compliant datasets or need tutorials on BIDS, you can look at this [BIDS Starter Kit](https://github.com/INCF/bids-starter-kit/).
+     If you need to create [BIDS](http://bids.neuroimaging.io/) compliant datasets or need tutorials on [BIDS](http://bids.neuroimaging.io/), you can look at this [BIDS Starter Kit](https://github.com/INCF/bids-starter-kit/).
 
 ## Clinica command-line interface
 
@@ -75,9 +75,9 @@ If you execute `clinica run --help`, you can see the list of `modality-pipeline`
 
 ### `clinica convert`
 
-These tools allow you to convert unorganized datasets from publicly available neuroimaging studies into a BIDS hierarchy.
-Clinica currently includes converters for [ADNI](http://adni.loni.usc.edu/), [AIBL](https://aibl.csiro.au) and [OASIS](http://www.oasis-brains.org).
-See [here](../DatabasesToBIDS) for more details.
+These tools allow you to convert unorganized datasets from publicly available neuroimaging studies into a [BIDS](http://bids.neuroimaging.io/) hierarchy.
+Clinica currently includes converters for [ADNI](http://adni.loni.usc.edu/), [AIBL](https://aibl.csiro.au), [NIFD](http://4rtni-ftldni.ini.usc.edu/), [OASIS](http://www.oasis-brains.org), [UK Biobank](https://www.ukbiobank.ac.uk/), and [GENFI](https://www.genfi.org).
+See [here](../Converters/ADNI2BIDS) for more details.
 
 ### `clinica iotools`
 
@@ -108,7 +108,7 @@ It can be also the input folder containing the dataset in a [CAPS](../CAPS/Intro
 
 You will see the `GROUP_LABEL` argument when working on any group-wise analysis (e.g. template creation from a list of subjects, statistical analysis).
 This is simply a label name that will define the  group of subjects used for this analysis.
-It will be written in your output CAPS folder, for possible future reuses.
+It will be written in your output [CAPS](../CAPS/Introduction) folder, for possible future reuses.
 For example, an `AD` group ID label could be used when creating a template for a group of Alzheimer’s disease patients.
 Any time you would like to use this `AD` template you will need to provide the group ID used to identify the pipeline output obtained from this group.
 You might also use `CNvsAD`, for instance, as group ID for a statistical group comparison between patients with Alzheimer's disease (`AD`) and cognitively normal (`CN`) subjects.

docs/index.md

@@ -70,7 +70,7 @@ Installation instructions are available [here](./ICMClusterInstallation).
 
 ### Dataset converters (`clinica convert`)
 
-Clinica provides tools to curate several publicly available neuroimaging datasets and convert them to BIDS namely:
+Clinica provides tools to curate several publicly available neuroimaging datasets and convert them to [BIDS](BIDS) namely:
 
 - `adni-to-bids` - [ADNI: Alzheimer’s Disease Neuroimaging Initiative](Converters/ADNI2BIDS)
 - `aibl-to-bids` - [AIBL: Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing](Converters/AIBL2BIDS)