From f563e14108222b9c96d32a4da15d7f7e2282f13c Mon Sep 17 00:00:00 2001 From: AliceJoubert <158147135+AliceJoubert@users.noreply.github.com> Date: Tue, 10 Sep 2024 14:55:55 +0200 Subject: [PATCH] [DOC] Refactor Third-Party documentation page (#1288) * Test tab link * Testing 2 * Testing 3 * Refactoring complete * Changes upon suggestions * link test * link test2 * Fix table * Fix links * Fix link git add docs/Third-party.md * Small fix * Change info points --- docs/Converters/ADNI2BIDS.md | 3 +- docs/Converters/AIBL2BIDS.md | 3 +- docs/Converters/GENFItoBIDS.md | 3 +- docs/Converters/NIFD2BIDS.md | 3 +- docs/Third-party.md | 357 ++++++++++++++++----------------- docs/css/clinica.css | 63 ++++++ mkdocs.yml | 3 + 7 files changed, 244 insertions(+), 191 deletions(-) diff --git a/docs/Converters/ADNI2BIDS.md b/docs/Converters/ADNI2BIDS.md index 42aa980a2..c657c9771 100644 --- a/docs/Converters/ADNI2BIDS.md +++ b/docs/Converters/ADNI2BIDS.md @@ -18,8 +18,7 @@ ## Dependencies -If you only installed the core of Clinica, this pipeline needs the installation of the **dcm2niix** DICOM to NIfTI converter. -You can find how to install these software packages on the [installation](../../#installing-clinica-from-source) page. +If you only [installed the core of Clinica](../Installation.md), this pipeline needs the installation of the [**dcm2niix**](../Third-party.md#dcm2nix) DICOM to NIfTI converter. ## Downloading ADNI diff --git a/docs/Converters/AIBL2BIDS.md b/docs/Converters/AIBL2BIDS.md index a6eb31685..5f48eddcb 100644 --- a/docs/Converters/AIBL2BIDS.md +++ b/docs/Converters/AIBL2BIDS.md @@ -21,8 +21,7 @@ ## Dependencies -If you only installed the core of Clinica, this pipeline needs the installation of the **dcm2niix** DICOM to NIfTI converter. -You can find how to install these software packages on the [installation](../../#installing-clinica-from-source) page. +If you only [installed the core of Clinica](../Installation.md), this pipeline needs the installation of the [**dcm2niix**](../Third-party.md#dcm2nix) DICOM to NIfTI converter. ### Downloading AIBL diff --git a/docs/Converters/GENFItoBIDS.md b/docs/Converters/GENFItoBIDS.md index 51b3a7904..c58dacb35 100644 --- a/docs/Converters/GENFItoBIDS.md +++ b/docs/Converters/GENFItoBIDS.md @@ -6,11 +6,12 @@ ## Dependencies -If you installed the core of Clinica, this converter needs the `dcm2niix` package. +If you only [installed the core of Clinica](../Installation.md), this pipeline needs the installation of the [**dcm2niix**](../Third-party.md#dcm2nix) DICOM to NIfTI converter. ## Supported modalities Please note that this converter currently processes the following modalities : + - T1W - T2W - DWI diff --git a/docs/Converters/NIFD2BIDS.md b/docs/Converters/NIFD2BIDS.md index 9733769aa..36088045a 100644 --- a/docs/Converters/NIFD2BIDS.md +++ b/docs/Converters/NIFD2BIDS.md @@ -7,8 +7,7 @@ ## Dependencies -If you only installed the core of Clinica, this pipeline needs the installation of the **dcm2niix** DICOM to NIfTI converter. -You can find how to install these software packages on the [installation](../../#installing-clinica-from-source) page. +If you only [installed the core of Clinica](../Installation.md), this pipeline needs the installation of the [**dcm2niix**](../Third-party.md#dcm2nix) DICOM to NIfTI converter. ## Downloading NIFD diff --git a/docs/Third-party.md b/docs/Third-party.md index 44b526ef6..1f7d5edfd 100644 --- a/docs/Third-party.md +++ b/docs/Third-party.md @@ -1,222 +1,222 @@ # Third-party software -## Converters +## Environment variables set-up -Some converters require a recent version of [dcm2niix](https://github.com/rordenlab/dcm2niix) to transform DICOM files into NIfTI: +As you will see on this page, environment variables are often needed in order to configure some third-party software installations. -| | dcm2niix | -|:------------------|:--------:| -| `adni-to-bids` | x | -| `aibl-to-bids` | x | -| `nifd-to-bids` | x | -| `oasis-to-bids` | | +1. Run the provided `export` and `source` commands in your terminal. Environment variables will be defined only for the duration of your session, +and will be lost if you re-launch your terminal. -Please check the installation instructions for all platforms [here](https://github.com/rordenlab/dcm2niix#install). + ??? info "Learn how to set environment variables" + - `export var_name = value` : defines an environment variable as value and makes it accessible to other processes started from the terminal. + - `source file` : used to read/execute a file, for example one where configurations are set -Clinica requires dcm2niix version `1.0.20190902` or later. +2. In order to define these variables permanently, you need to manually edit the configuration file associated to your shell. -## Pipeline-specific interfaces + If you are using `bash`, it can be `~/.bashrc` or `~/.bash_profile`, if you are using `zsh`, it should be `~/.zshrc`. -Not all the following dependencies are necessary to install and run Clinica. -You may want to only install the software packages used by certain pipelines of Clinica. -Pipelines' specific dependencies are listed below: +!!! danger "Provided command lines should be adapted" + **Please** do not copy/paste the provided commands without adapting them to your system and without testing them. + Most paths provided here require to be adapted to your system and depend on how you installed the software. + + A good approach is to verify that the different paths you want to assign to a variable exist first : -| | ANTs | Convert3D | FreeSurfer | FSL | ITK | Matlab | MRtrix3 | PETPVC | SPM | -|:-------------------------|:----:|:---------:|:----------:|:---:|:---:|:------:|:-------:|:------:|:---:| -| `t1-volume-*` | | | | | | x | | | x | -| `t1-freesurfer` | | | x | | | | | | | -| `dwi-preprocessing-*` | x | x | | x | | | x | | | -| `dwi-dti` | x | | | x | | | x | | | -| `dwi-connectome` | x | | x | x | | | x | | | -| `pet-surface` | | | | x | x* | | | x* | x | -| `pet-volume` | | | | | x* | x | | x* | x | -| `statistics-surface` | | | | | | x | | | | -| `machine-learning-*` | | | | | | | | | | + → If they do, then try running the `export` and `source` **(step 1. above)** commands in your terminal. Verify that the software or the pipeline you want runs as expected. + + → If this works, then consider modifying your shell configuration file **(step 2. above)** to have these variables automatically defined on every session. -!!! note "CAT12 toolbox" - Starting from Clinica `v0.3.7`, the [**CAT12**](http://dbm.neuro.uni-jena.de/cat/) toolbox is no longer needed for the `t1-volume` and `pet-volume` pipelines. - For previous versions of Clinica, you will need to download the latest version of the toolbox [here](http://dbm.neuro.uni-jena.de/cat/index.html#DOWNLOAD) and follow the instructions to ensure that your `cat12` folder is located in your `spm/toolbox` folder. -_*You only need to install ITK if you plan to perform partial volume correction using PETPVC._ +## Converters -Depending on the architecture and OS of your system, setup of third party libraries can change. -Please refer to each tool’s website for installation instructions: +Some converters require **dcm2niix** to transform DICOM files into NIfTI : -### Environment variables setup +
+ adni-to-bids + aibl-to-bids + genfi-to-bids + nifd-to-bids + ukb-to-bids +
-When installing some of the third party software, environment variables might be needed in order to configure some installations. +### DCM2NIX -If you simply run the `export` and `source` commands in your terminal, these environment variables will be defined only for the duration of your session, and will be lost if you re-launch your terminal. +!!! warning "Version required" + Clinica requires dcm2niix version `1.0.20190902` or later. -In order to define these variables permanently, you need to manually edit the configuration file associated to your shell. +Please check the installation instructions for all platforms on [dcm2niix Git repository](https://github.com/rordenlab/dcm2niix#install). -If you are using `bash`, it can be `~/.bashrc` or `~/.bash_profile`, if you are using `zsh`, it should be `~/.zshrc`. -!!! note "test before" - Please do not copy/paste the provided commands without adapting them to your system and without testing them. - Most paths provided here require to be adapted to your system, and also depends on how you installed the software. - A good approach is to verify that the different paths you want to assign to a variable exist first. - If they do, then try running the `export` and `source` commands in your terminal, and verify that the software run as expected. - You can also verify that the pipeline you want to use is also running as expected. - If this works, then consider modifying your shell configuration file to have these variables automatically defined on every session. +## Pipelines -### ANTs +
+Some, but not all pipelines use specific third-party software. Depending on your usage of Clinica, you will need to install additional packages. +Specific dependencies are listed below (1) : +
-#### Installation +1. If not listed, the pipeline does not require any additional dependency outside Clinica. -To install `ANTs`, download it from [here](https://github.com/stnava/ANTs/releases) and follow the instructions on the `ANTs` [wiki](https://github.com/stnava/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS). +
-#### Configuration +| | ANTs | Convert3D | FreeSurfer | FSL | ITK | Matlab | MRtrix3 | PETPVC | SPM | +|:-------------------:|:----:|:---------:|:----------:|:---:|:---:|:------:|:-------:|:------:|:---:| +| Anat > Linear | ✓∘ | | | | | | | | | +| Anat > Volume | | | | | | ✓ | | | ✓ | +| Anat > FreeSurfer | | | ✓ | | | | | | | +| DWI > Preprocessing | ✓ | ✓ | | ✓ | | | ✓ | | | +| DWI > DTI | ✓ | | | ✓ | | | ✓ | | | +| DWI > Connectome | | | ✓ | ✓ | | | ✓ | | | +| PET > Linear | ✓ | | | | | | | | | +| PET > Surface | | | ✓ | ✓ | ✓⟡ | ✓ | | ✓⟡ | ✓ | +| PET > Volume | | | | | ✓⟡ | ✓ | | ✓⟡ | ✓ | +| Stats > Surface | | | ✓ | | | | | | | +| Stats > Volume | | | | | | ✓ | | | ✓ | -We strongly recommend installing `ANTs >= 2.5.0` from which **no environment variable are needed**. +
-Nonetheless, if you are using an older version of `ANTs`, make sure to have the following environment variables defined: +- *✓∘ : for anatomical linear pipelines there is also the possibility to use ANTsPy instead of ANTs since Clinica `v0.9.0`* +- *✓⟡ : you only need to install ITK if you plan to perform partial volume correction using PETPVC.* -```bash -export ANTSPATH="/path/to/your/ANTs/" -export PATH=${ANTSPATH}:${PATH} -``` +??? warning "CAT12 toolbox and Clinica < `v0.3.7`" + Starting from Clinica `v0.3.7`, the [**CAT12**](http://dbm.neuro.uni-jena.de/cat/) toolbox is no longer needed for the `t1-volume` and `pet-volume` pipelines. + For previous versions of Clinica, you will need to download the latest version of the toolbox [here](http://dbm.neuro.uni-jena.de/cat/index.html#DOWNLOAD) and follow the instructions to ensure that your `cat12` folder is located in your `spm/toolbox` folder. -### Convert3D +Depending on the architecture and OS of your system, setup of third party libraries can change. +Please refer to each tool’s website for installation instructions : +___ + +### ANTs -You can find more details about `Convert3D` [here](http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D). +To install `ANTs`, download it from [ANTs release list](https://github.com/stnava/ANTs/releases) and follow the instructions on [ANTs wiki](https://github.com/stnava/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS). -#### Installation +=== "`ANTs >= 2.5.0` 🔺" + We **strongly** recommend installing `ANTs >= 2.5.0` from which **no environment variable are needed**. -You have two options to install `Convert3D`: +=== "`ANTs < 2.5.0`" + Nonetheless, if you are using an older version of `ANTs`, make sure to have the following environment variables defined: + + ```{ .bash .copy } + export ANTSPATH="/path/to/your/ANTs/" + export PATH=${ANTSPATH}:${PATH} + ``` -- [Use pre-built binaries](http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.C3D). -- [Use the official conda package](https://anaconda.org/conda-forge/convert3d). +___ -### Freesurfer +### Convert3D -You can find more details about `Freesurfer` [here](http://surfer.nmr.mgh.harvard.edu/). +You can find more details about `Convert3D` on their [website](http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D). There are +two options to install it : -#### Installation +- [Use pre-built binaries](http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.C3D). +- [Use the official conda package](https://anaconda.org/conda-forge/convert3d). -##### On Linux +___ -Download and install `FreeSurfer` following the instructions on the [wiki](http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall). +### FreeSurfer -!!! note - Please note that on Ubuntu you will need to install the packages `tcsh` and `libjpeg62` ( a `sudo apt-get install tcsh libjpeg62` should do the job). +You can find more details about `FreeSurfer` on their [website](http://surfer.nmr.mgh.harvard.edu/). To install it : -##### On MacOS +=== "Linux" + Download and install `FreeSurfer` following the instructions on the [wiki](http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall). -Download it from [here](http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) and follow the instructions on the `FreeSurfer` [wiki](https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall). + !!! warning + Please note that on Ubuntu you will need to install the packages `tcsh` and `libjpeg62` ( a `sudo apt-get install tcsh libjpeg62` should do the job). + +=== "MacOS" + Download it from [here](http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) and follow the instructions on the `FreeSurfer` [wiki](https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall). -#### Configuration Make sure to have the following environment variables defined: -```bash +```{ .bash .copy } export FREESURFER_HOME="/Applications/freesurfer" source ${FREESURFER_HOME}/SetUpFreeSurfer.sh &> /dev/null ``` +___ + ### FSL We recommend installing [**FSL 6.0**](https://fsl.fmrib.ox.ac.uk/). -#### Installation - -##### On Linux - -Download it from [here](https://fsl.fmrib.ox.ac.uk/fsldownloads) and follow the instructions on the [FSL wiki](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux). - -##### On MacOS +=== "Linux" + Download it from [here](https://fsl.fmrib.ox.ac.uk/fsldownloads) and follow the instructions on the [FSL wiki](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux). -Download it from [here](https://fsl.fmrib.ox.ac.uk/fsldownloads) and follow the instructions on the [FSL wiki](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/MacOsX). - -#### Configuration - -##### On Linux - -Make sure to have the following environment variables defined: - -```bash -export FSLDIR="/usr/share/fsl/6.0" -export PATH="${FSLDIR}/bin":${PATH} -source ${FSLDIR}/etc/fslconf/fsl.sh -``` + Make sure to have the following environment variables defined: + ```{ .bash .copy } + export FSLDIR="/usr/share/fsl/6.0" + export PATH="${FSLDIR}/bin":${PATH} + source ${FSLDIR}/etc/fslconf/fsl.sh + ``` -##### On MacOS +=== "MacOS" + Download it from [here](https://fsl.fmrib.ox.ac.uk/fsldownloads) and follow the instructions on the [FSL wiki](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/MacOsX). -Make sure to have the following environment variables defined: + Make sure to have the following environment variables defined: + ```{ .bash .copy } + export FSLDIR="/usr/local/fsl" + export PATH="${FSLDIR}/bin":${PATH} + source ${FSLDIR}/etc/fslconf/fsl.sh + ``` -```bash -export FSLDIR="/usr/local/fsl" -export PATH="${FSLDIR}/bin":${PATH} -source ${FSLDIR}/etc/fslconf/fsl.sh -``` +___ ### ITK -You can find more details about `ITK` [here](https://itk.org/). - -#### Installation +You can find more details about `ITK` on their [website](https://itk.org/). To install it : -##### On Linux +=== "Linux" + Follow the instructions on the [ITK blog](https://blog.kitware.com/itk-packages-in-linux-distributions/). -Follow the instructions on the [ITK blog](https://blog.kitware.com/itk-packages-in-linux-distributions/). +=== "MacOS" + Follow the instructions on the [ITK blog](https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/). -##### On MacOS - -Follow the instructions on the [ITK blog](https://blog.kitware.com/kitware-packages-on-os-x-with-homebrew/). +___ ### MRtrix3 -You can find more details about `MRtrix3` [here](http://www.mrtrix.org). - -#### Installation - -You can find the official instructions on the `MRtrix` [website](https://www.mrtrix.org/download/). - -##### On Linux +You can find more details about `MRtrix3` on their [website](http://www.mrtrix.org), including +official instructions for [downloading](https://www.mrtrix.org/download/). -You have basically two options: +=== "Linux" + You have basically two options: -- [Use the official conda package](https://www.mrtrix.org/download/linux-anaconda/). -- [Build MRtrix3 from source](https://mrtrix.readthedocs.io/en/latest/installation/build_from_source.html#linux). + - [Use the official conda package](https://www.mrtrix.org/download/linux-anaconda/). + - [Build MRtrix3 from source](https://mrtrix.readthedocs.io/en/latest/installation/build_from_source.html#linux). -!!! note - Note that using the conda package should be easier in most cases. + !!! tip + Note that using the conda package should be easier in most cases. -##### On MacOS +=== "MacOS" -- [Use the official conda package](https://www.mrtrix.org/download/macos-anaconda/). -- [Use the MacOS pre-compiled application package installer](https://www.mrtrix.org/download/macos-application/). -- [Use the Homebrew formula](https://github.com/MRtrix3/homebrew-mrtrix3) (although large dependencies such as `XCode` and `Qt5` are required). + - [Use the official conda package](https://www.mrtrix.org/download/macos-anaconda/). + - [Use the MacOS pre-compiled application package installer](https://www.mrtrix.org/download/macos-application/). + - [Use the Homebrew formula](https://github.com/MRtrix3/homebrew-mrtrix3) (although large dependencies such as `XCode` and `Qt5` are required). -!!! note - As for Linux, note that using the conda package should be easier in most cases. +___ ### Matlab -You can find more details about `Matlab` [here](https://fr.mathworks.com/products/matlab/). +You can find more details about `Matlab` on their [website](https://fr.mathworks.com/products/matlab/). -!!! note - Note that using `Matlab` requires having a valid license which might be available through your university or institution. - -#### Configuration +!!! warning + Note that using `Matlab` requires having a **valid license** which might be available through your university or institution. Make sure to have the following environment variables defined: -```bash +```{ .bash .copy } export MATLAB_HOME="/path/to/your/matlab/bin/" export PATH=${MATLAB_HOME}:${PATH} export MATLABCMD="${MATLAB_HOME}/matlab" ``` -### PETPVC - -You can find more details about `PETPVC` [here](https://github.com/UCL/PETPVC). +___ -#### Installation +### PETPVC -You can find the official instructions in the README of [this page](https://github.com/UCL/PETPVC). +You can find more details about `PETPVC` on their [website](https://github.com/UCL/PETPVC), +including official instructions for downloading on their [Github](https://github.com/UCL/PETPVC). You have basically three options: @@ -224,58 +224,52 @@ You have basically three options: - [Use the official conda package](https://anaconda.org/conda-forge/petpvc). - [Build from source](https://github.com/UCL/PETPVC?tab=readme-ov-file#installation-from-source-instructions). -!!! note - If building from source, do not forget to compile in RELEASE mode, otherwise, partial volume correction will be very slow. - -### SPM12 - -You can find more details about `SPM12` [here](http://www.fil.ion.ucl.ac.uk/spm/). +!!! tip + If building from source, do not forget to compile in **RELEASE** mode, otherwise, partial volume correction will be very slow. -Note that `SPM12` works with [Matlab](#matlab) such that clinica pipelines which require `SPM12`, will also need a `Matlab` installation. +___ -If you cannot install `Matlab`, you can install [SPM standalone](#spm12-standalone). - -#### Installation - -##### On Linux - -Download the latest version [here](http://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip) and follow the instructions on the [SPM wiki](https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux). - -##### On MacOS - -Download the latest version [here](http://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip) and follow the instructions on the [SPM wiki](https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)). - -!!! note - For systems running on MacOS Big Sur, a [development version of SPM12](https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/) as well as a more recent release of the MCR (minimum 2019a) are required. +### SPM12 -#### Configuration +!!! warning "SPM12 and Matlab" + Note that `SPM12` works with [Matlab](#matlab) such that Clinica pipelines which require `SPM12`, will also need a `Matlab` installation. + If you cannot install `Matlab`, you can install [SPM standalone](#spm12-standalone). -Make sure to have the following environment variable defined: +You can find more details about `SPM12` on their [website](http://www.fil.ion.ucl.ac.uk/spm/). To install it : -```bash -export SPM_HOME="/path/to/your/spm12" -``` +=== "Linux" + Download the latest version [here](http://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip) and follow the instructions on the [SPM wiki](https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux). -You must also add `SPM` to the `MATLAB` path variable if you installed it as a toolbox. +=== "MacOS" + Download the latest version [here](http://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip) and follow the instructions on the [SPM wiki](https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)). -To do so, add the following line to your `startup.m` file located in your *initial working folder*, by default `~/Documents/MATLAB` (see [here](https://fr.mathworks.com/help/matlab/ref/startup.html) for more details). + ??? warning "MacOS Big Sur" + For systems running on MacOS Big Sur, a [development version of SPM12](https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/) as well as a more recent release of the MCR (minimum 2019a) are required. -If the file does not exist, you can create it and type inside: -```matlab -addpath('/path/to/your/spm12'); -``` - -You can also replace the previous line by the following, assuming the `$SPM_HOME` environment variable is set in your `~/.bashrc` file. - -```matlab -[~, spmhome] = system('source ~/.bashrc > /dev/null; echo $SPM_HOME;'); -spmhome = strsplit(spmhome,'\n'); -addpath(spmhome{end-1}); -``` +1. Make sure to have the following environment variable defined: + ```{ .bash .copy } + export SPM_HOME="/path/to/your/spm12" + ``` -!!! Note - `zsh` shell users will have to replace `~/.bashrc` by `~/.zshrc`. + 2. You must also add `SPM` to the `MATLAB` path variable if you installed it as a toolbox. + - First, verify a `startup.m` file exists in your *initial working folder*, by default `~/Documents/MATLAB` (see [here](https://fr.mathworks.com/help/matlab/ref/startup.html) for more details). + If the file does not exist, you can create it. + - Then, type inside: + ```matlab + addpath('/path/to/your/spm12'); + ``` + **OR**, assuming the `$SPM_HOME` environment variable is set in your `~/.bashrc` file : + ```matlab + [~, spmhome] = system('source ~/.bashrc > /dev/null; echo $SPM_HOME;'); + spmhome = strsplit(spmhome,'\n'); + addpath(spmhome{end-1}); + ``` + + !!! warning + `zsh` shell users will have to replace `~/.bashrc` by `~/.zshrc`. + +___ ### SPM12 standalone @@ -284,13 +278,9 @@ If you want to install `SPM12` without installing [Matlab](#matlab), you will ne - The Matlab runtime (often abbreviated into MCR), for which no license is required. - The SPM standalone itself. -#### Installation - You can find details on how to install these on [this page](https://www.fil.ion.ucl.ac.uk/spm/docs/installation/standalone/). -#### Configuration - -!!! note +!!! tip "Verify your environment variables" If you followed the installation instructions, you should have set the environment variable `$LD_LIBRARY_PATH`. In addition, you need to define the following environment variables: @@ -300,12 +290,12 @@ export MCR_HOME="/path/to/your/MCR/" export SPMSTANDALONE_HOME="/path/to/your/spmstandalone/home/" ``` -## Autocompletion +### Autocompletion -!!! Note +!!! warning "Autocompletion for `zsh` shell users" `zsh` shell users will have to add this right before the last line of their configuration file to enable autocompletion in Clinica: ```bash @@ -313,4 +303,3 @@ eval "$(register-python-argcomplete clinica)" --> bashcompinit source ~/.bash_completion.d/python-argcomplete.sh ``` - diff --git a/docs/css/clinica.css b/docs/css/clinica.css index 6f494ddf0..05497544c 100644 --- a/docs/css/clinica.css +++ b/docs/css/clinica.css @@ -1,3 +1,4 @@ +body {text-align: justify} .md-typeset .codehilite, .md-typeset .highlight, code { color: #c7254e; @@ -41,3 +42,65 @@ h3, .h3, .md-typeset h3 { font-weight: 600; margin: 1.6rem 0 1.6rem; } + +.grid a { + color: #333; /* Link color */ + text-align: center; + font-size:12px; +} + + +.md-typeset__table { + width: 100%; +} + +.md-typeset table:not([class]) { + display: table; +} + + +.third_party_table table { + border-collapse: collapse; + table-layout: fixed; + } + +.third_party_table td, th { + border: 0px solid #ddd; + padding: 0px 0px; + text-align: center, + } + +.third_party_table tr:hover { + color:#ff6600; + } + +.third_party_table th:nth-child(1) { + width: 20%; + } +.third_party_table th:nth-child(2) { + width: 8%; + } +.third_party_table th:nth-child(3) { + width: 11%; + } +.third_party_table th:nth-child(4) { + width: 11%; + } +.third_party_table th:nth-child(5) { + width: 6%; + } +.third_party_table th:nth-child(6) { + width: 6%; + } + .third_party_table th:nth-child(7) { + width: 10%; + } +.third_party_table th:nth-child(8) { + width: 10%; + } +.third_party_table th:nth-child(9) { + width: 10%; + } +.third_party_table th:nth-child(10) { + width: 8%; + } diff --git a/mkdocs.yml b/mkdocs.yml index bb241d58a..c2428bd73 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -25,6 +25,8 @@ theme: accent: light blue features: - content.tooltips + - content.tabs.link + - navigation.top # Version panel extra_javascript: @@ -61,6 +63,7 @@ markdown_extensions: - md_in_html - abbr - attr_list + - md_in_html - pymdownx.snippets: base_path: docs auto_append: