From 5b1c20d0cdd3bd557c35d288d98119aee922f7d7 Mon Sep 17 00:00:00 2001 From: Siemon de Lange Date: Mon, 10 Jul 2023 14:13:36 +0200 Subject: [PATCH] Improve Download section --- docs/installation.rst | 43 +++++++------------------------------------ 1 file changed, 7 insertions(+), 36 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index 0d8fe62..0b3d08c 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -7,53 +7,24 @@ Installation Download -------------------- -Compiled binaries of the latest toolbox version: +**CATO executable:** Download the compiled binaries of the latest CATO version from the following links: .. raw:: html :file: ../_static/emailform.html -and all source code is available on `the GitHub repository `_. CATO is also available as Docker image on `Docker Hub `_. +**Source code**: Access the source code of CATO from the `GitHub repository `_. -Example configuration files can be downloaded (or use the :ref:`online Configuration Assistant `): +**Docker image:** CATO is also available as a Docker image on `Docker Hub `_. + +**Example configuration files:** Example configuration files can be downloaded from the links below (or use the :ref:`online Configuration Assistant ` to customize your own configuration file): - :download:`Example functional configuration file <../_static/configuration_files/configuration_functional_example.json>` - :download:`Example structural configuration file <../_static/configuration_files/configuration_structural_example.json>` -Additional software often used with CATO are described in the :ref:`Installation additional software` section. - -.. toggle-header:: - :header: **Release notes** - - Older versions of CATO (binaries and source-code) can be downloaded from `the CATO repository on Github `_ and older versions of this documentation website (corresponding to older CATO versions) can be downloaded from `the CATO docs repository on GitHub `_ . - - - Version 3.2.1 (13 February 2023) - - Fixes fMRI bandpass filter artefacts at the beginning and end of the filtered rs-fMRI time series. - - Full Changelog: https://github.com/dutchconnectomelab/CATO/compare/v3.2.0...v3.2.1 - - - Version 3.2.0 (30 November 2022) - - Introduces a test framework for continuous integration. - - Lets users specify the functional connectivity measure (e.g. Pearson correlations or Pearson partial correlations). - - Preprocessing scripts are now compatible with FreeSurfer version 7. - - Removes dependencies on FreeSurfer and FSL in the MATLAB functions. FreeSurfer and FSL are now only used in the preprocessing and parcellation scripts that are provided by the user. - - Fixes various bugs (e.g. in the readTrk function, the iRESTORE threshold assistant). - - Improves various features (e.g. error handling and the check on the toolboxes installed in MATLAB). - - Full Changelog: https://github.com/dutchconnectomelab/CATO/commits/v3.2.0 - - - Version 3.1.2 (28 May 2021) - - Fixes minor issue that let MATLAB utilize all available computational threads, but which is undesirable when running multiple instances of CATO in parallel. This minor patch introduces the parameter :term:`maxNumberCompThreads` (default = 1) that lets the user set the maximum number of used computational threads. - - - Version 3.1.1 (22 March 2021) - - Fixes minor issue that caused in some configurations a "non-existent field" error. This is a minor patch does not affect any MRI processing. This error can also be fixed by adding a variable that specifies the lutFile in the collect_region_properties step in the configuration file: :: +**Additional software:** Additional software, such as MATLAB MCR, FreeSurfer and FSL, are (often) needed for connectome processing with CATO. Refer to the :ref:`Installation additional software` section for more details. - "collect_region_properties":{ - "lutFile": "TEMPLATESDIR/TEMPLATE/TEMPLATE.annot.ctab" - } +**Archived versions:** Older versions of CATO, along with their associated release notes, are available from the `CATO repository on Github `_. - - Version 3.1 (16 March 2021) - - Memory usage is reduced in the diffusion reconstruction step when correcting for gradient nonlinearities. - - Fixes an issue with the lausanne parcellations that nodes are incorrectly ordered and labeled. This issue affected only version 3.0 and the lausanne120, lausanne250 and lausanne500 parcellations (the Desikan-Killiany, aparc, parcellation is not affected). - - Fiber tracker seeds are now better distributed and compatible with high-quality DWI data. - - The CSD and DTI diffusion reconstruction methods are further improved to give better diffusion profile reconstructions. Installation executable ------------------------------------------------------------