some more

aramis-lab · Nov 16, 2023 · 0adf65d · 0adf65d
1 parent 3ba23ee
commit 0adf65d
Show file tree

Hide file tree

Showing 2 changed files with 19 additions and 17 deletions.
diff --git a/docs/BIDS.md b/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:

diff --git a/docs/Installation.md b/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: