From 0adf65d3ea40bcec35e8e17bcf05ab5b1f9ceed6 Mon Sep 17 00:00:00 2001 From: NicolasGensollen Date: Thu, 16 Nov 2023 10:08:45 +0100 Subject: [PATCH] some more --- docs/BIDS.md | 19 +++++++++++-------- docs/Installation.md | 17 ++++++++--------- 2 files changed, 19 insertions(+), 17 deletions(-) diff --git a/docs/BIDS.md b/docs/BIDS.md index 5d10b0a2e..072f2c251 100644 --- 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 index cff2b664f..2343d029e 100644 --- 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: @@ -29,10 +30,10 @@ 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 @@ -40,7 +41,7 @@ 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: