Edit README file with new installation instructions

README.md

@@ -40,83 +40,129 @@
 
 ## About The Project
 
-Clinica is a software platform for clinical research studies involving patients with neurological and psychiatric diseases and the acquisition of multimodal data (neuroimaging, clinical and cognitive evaluations, genetics...), most often with longitudinal follow-up.
-
-Clinica is command-line driven and written in Python. It uses the [Nipype](https://nipype.readthedocs.io/) system for pipelining and combines widely-used software packages for neuroimaging data analysis ([ANTs](http://stnava.github.io/ANTs/), [FreeSurfer](https://surfer.nmr.mgh.harvard.edu/), [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki), [MRtrix](https://www.mrtrix.org/), [PETPVC](https://github.com/UCL/PETPVC), [SPM](https://www.fil.ion.ucl.ac.uk/spm/)), machine learning ([Scikit-learn](https://scikit-learn.org/stable/)) and the [BIDS standard](http://bids-specification.readthedocs.io/) for data organization.
-
-Clinica provides tools to convert publicly available neuroimaging datasets into BIDS, namely:
+Clinica is a software platform for clinical research studies involving patients
+with neurological and psychiatric diseases and the acquisition of multimodal
+data (neuroimaging, clinical and cognitive evaluations, genetics...), most
+often with longitudinal follow-up.
+
+Clinica is command-line driven and written in Python. It uses the
+[Nipype](https://nipype.readthedocs.io/) system for pipelining and combines
+widely-used software packages for neuroimaging data analysis
+([ANTs](http://stnava.github.io/ANTs/),
+[FreeSurfer](https://surfer.nmr.mgh.harvard.edu/),
+[FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki),
+[MRtrix](https://www.mrtrix.org/), [PETPVC](https://github.com/UCL/PETPVC),
+[SPM](https://www.fil.ion.ucl.ac.uk/spm/)), machine learning
+([Scikit-learn](https://scikit-learn.org/stable/)) and the [BIDS
+standard](http://bids-specification.readthedocs.io/) for data organization.
+
+Clinica provides tools to convert publicly available neuroimaging datasets into
+BIDS, namely:
 
 - [ADNI: Alzheimer’s Disease Neuroimaging Initiative](http://www.clinica.run/doc/Converters/ADNI2BIDS)
 - [AIBL: Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing](http://www.clinica.run/doc/Converters/AIBL2BIDS)
 - [NIFD: Neuroimaging in Frontotemporal Dementia](http://www.clinica.run/doc/Converters/NIFD2BIDS)
 - [OASIS: Open Access Series of Imaging Studies](http://www.clinica.run/doc/Converters/OASIS2BIDS)
 
-Clinica can process any BIDS-compliant dataset with a set of complex processing pipelines involving different software packages for the analysis of neuroimaging data (T1-weighted MRI, diffusion MRI and PET data). It also provides integration between feature extraction and statistics, machine learning or deep learning.
+Clinica can process any BIDS-compliant dataset with a set of complex processing
+pipelines involving different software packages for the analysis of
+neuroimaging data (T1-weighted MRI, diffusion MRI and PET data). It also
+provides integration between feature extraction and statistics, machine
+learning or deep learning.
 
 ![ClinicaPipelines](http://www.clinica.run/img/clinica_pipelines.png)
 
 <p align="center">
   <i>Current pipelines are indicated in blue while new or updated pipelines are indicated in purple (will be released in Summer 2020).</i>
 </p>
 
-Clinica is also showcased as a framework for the reproducible classification of Alzheimer's disease using [machine learning](https://github.com/aramis-lab/AD-ML) and [deep learning](https://github.com/aramis-lab/AD-DL).
+Clinica is also showcased as a framework for the reproducible classification of
+Alzheimer's disease using [machine
+learning](https://github.com/aramis-lab/AD-ML) and [deep
+learning](https://github.com/aramis-lab/AD-DL).
 
 
 
 ## Getting Started
 > Full instructions for installation and additional information can be found in
 the [user documentation](http://www.clinica.run/doc).
 
-Clinica currently supports macOS and Linux. It can be installed:
+Clinica currently supports macOS and Linux. It can be installed by typing the
+following command:
 
-- With `conda` (recommended):
 ```sh
-conda create --name clinicaEnv python=3.6 clinica -c Aramislab -c conda-forge
+pip install clinica
 ```
 
-- With `pip` (needs Python 3.7)
+To avoid conflicts with other versions of the dependency packages installed by
+pip, it is strongly recommended to create a virtual environment before the
+installation.  For example, use
+[Conda](https://docs.conda.io/en/latest/miniconda.html), to create a virtual
+environment and activate it before installing clinica (you can also use
+`virtualenv`):
+
 ```sh
-pip install clinica
+conda create --name clinicaEnv python=3.7
+conda activate clinicaEnv
 ```
 
-- Using the [Developer installation](http://www.clinica.run/doc/Installation/#developer-installation)
-
-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 [page](http://www.clinica.run/doc/Third-party/) to determine which third-party libraries you need to install.
+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 [page](http://www.clinica.run/doc/Third-party/)
+to determine which third-party libraries you need to install.
 
 ## Example
 
-Diagram illustrating the Clinica pipelines involved when performing a group comparison of FDG PET data projected on the cortical surface between patients with Alzheimer's disease and healthy controls from the ADNI database:
+Diagram illustrating the Clinica pipelines involved when performing a group
+comparison of FDG PET data projected on the cortical surface between patients
+with Alzheimer's disease and healthy controls from the ADNI database:
 ![ClinicaExample](http://www.clinica.run/img/clinica_example.png)
-1. Clinical and neuroimaging data are downloaded from the ADNI website and data are converted into BIDS with the [`adni-to-bids` converter](http://www.clinica.run/doc/Converters/ADNI2BIDS).
-2. Estimation of the cortical and white surface is then produced by the [`t1-freesurfer` pipeline](http://www.clinica.run/doc/Pipelines/T1_FreeSurfer).
-3. FDG PET data can be projected on the subject’s cortical surface and normalized to the FsAverage template from FreeSurfer using the [`pet-surface` pipeline](http://www.clinica.run/doc/Pipelines/PET_Surface).
-4. TSV file with demographic information of the population studied is given to the [`statistics-surface` pipeline](http://www.clinica.run/doc/Pipelines/Stats_Surface) to generate the results of the group comparison.
+1. Clinical and neuroimaging data are downloaded from the ADNI website and data
+   are converted into BIDS with the [`adni-to-bids`
+   converter](http://www.clinica.run/doc/Converters/ADNI2BIDS).
+2. Estimation of the cortical and white surface is then produced by the
+   [`t1-freesurfer`
+   pipeline](http://www.clinica.run/doc/Pipelines/T1_FreeSurfer).
+3. FDG PET data can be projected on the subject’s cortical surface and
+   normalized to the FsAverage template from FreeSurfer using the
+   [`pet-surface` pipeline](http://www.clinica.run/doc/Pipelines/PET_Surface).
+4. TSV file with demographic information of the population studied is given to
+   the [`statistics-surface`
+   pipeline](http://www.clinica.run/doc/Pipelines/Stats_Surface) to generate
+   the results of the group comparison.
 
-> For more examples and details, please refer to the [Documentation](http://www.clinica.run/doc/).
+> For more examples and details, please refer to the
+> [Documentation](http://www.clinica.run/doc/).
 
 
 
 
 
 ## Support
 - [Report an issue on GitHub](https://github.com/aramis-lab/clinica/issues)
-- Use the [Clinica Google Group](https://groups.google.com/forum/#!forum/clinica-user) to ask for help!
+- Use the [Clinica Google
+  Group](https://groups.google.com/forum/#!forum/clinica-user) to ask for help!
 
 
 
 
 
 <!--
 ## Contributing
-We encourage you to contribute to Clinica! Please check out the [Contributing to Clinica guide](Contributing.md) for guidelines about how to proceed. Do not hesitate to ask questions if something is not clear for you, report an issue, etc.
+We encourage you to contribute to Clinica! Please check out the [Contributing
+to Clinica guide](Contributing.md) for guidelines about how to proceed. Do not
+hesitate to ask questions if something is not clear for you, report an issue,
+etc.
 -->
 
 
 
 
 ## License
 
-This software is distributed under the MIT License. See [license file](https://github.com/aramis-lab/clinica/blob/dev/LICENSE.txt) for more information.
+This software is distributed under the MIT License. See [license
+file](https://github.com/aramis-lab/clinica/blob/dev/LICENSE.txt) for more
+information.
 
 
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