Releases: Inria-Empenn/Anima-Scripts-Public
Anima scripts v3.3
Feature update release of Anima scripts
Anima scripts is a set of scripts that use Anima to perform complex preprocessing and core processing tasks on medical images. This repository is multi-platform for most scripts (as long as python is available for your system), except for atlasing scripts that require an OAR scheduler. If you are using Anima scripts for your research, please take the time to:
- Cite the relevant papers referenced in the documentation
- Add a sentence in your acknowledgments section or in the methods part of your paper referencing the RRID of Anima scripts: RRID:SCR_017072, and the one of Anima : RRID:SCR_017017
- if possible, add the link to Anima website: https://anima.irisa.fr
This new release contains the following updates:
- Add new EM based three tissues segmentation script
- Add large field of view brain masking option e.g. for newborn images
- temporary folders are now located in current folder and can be kept after script run
- bug correction in diffusion image preprocessing (siemens dicom handling)
- anima scripts now requires Anima v4.2 as the minimum version to run all scripts
More details on the scripts are available in the documentation.
Anima scripts v3.2
Feature update release of Anima scripts
Anima scripts is a set of scripts that use Anima to perform complex preprocessing and core processing tasks on medical images. This repository is multi-platform for most scripts (as long as python is available for your system), except for atlasing scripts that require an OAR scheduler. If you are using Anima scripts for your research, please take the time to:
- Cite the relevant papers referenced in the documentation
- Add a sentence in your acknowledgments section or in the methods part of your paper referencing the RRID of Anima scripts: RRID:SCR_017072, and the one of Anima : RRID:SCR_017017
- if possible, add the link to Anima website: https://anima.irisa.fr
This new release contains the following updates:
- add MS preprocessing script from the 2016 MS lesions segmentation challenge
- add short documentation of MS scripts
- correct bugs in T2 relaxometry and diffusion scripts
- correct bug in DTI atlasing script that was not using log-Euclidean metrics to fuse all images
- anima scripts now requires Anima v4.1.1 as the minimum version to run all scripts
More details on the scripts are available in the documentation.
Anima scripts v3.1
Feature update release of Anima scripts
Anima scripts is a set of scripts that use Anima to perform complex preprocessing and core processing tasks on medical images. This repository is multi-platform for most scripts (as long as python is available for your system), except for atlasing scripts that require an OAR scheduler. If you are using Anima scripts for your research, please take the time to:
- Cite the relevant papers referenced in the documentation
- Add a sentence in your acknowledgments section or in the methods part of your paper referencing the RRID of Anima scripts: RRID:SCR_017072, and the one of Anima : RRID:SCR_017017
- if possible, add the link to Anima website: https://anima.irisa.fr
This new release contains the following updates:
- add MS longitudinal preprocessing script for the 2021 MS new lesions segmentation challenge
- add patient specific pipeline for atlas based, along tract analysis of diffusion compartment models
- anima scripts now requires Anima v4.1 as the minimum version to run all scripts
More details on the scripts are available in the documentation.
Anima scripts v3.0.1
Bug fix release of Anima scripts
Anima scripts is a set of scripts that use Anima to perform complex preprocessing and core processing tasks on medical images. This repository is multi-platform for most scripts (as long as python is available for your system), except for atlasing scripts that require an OAR scheduler. If you are using Anima scripts for your research, please take the time to:
- Cite the relevant papers referenced in the documentation
- Add a sentence in your acknowledgments section or in the methods part of your paper referencing the RRID of Anima scripts: RRID:SCR_017072, and the one of Anima : RRID:SCR_017017
- if possible, add the link to Anima website: https://anima.irisa.fr
This new release contains the following updates:
- add configuration script to simplify installation
- minor fixes and improvements
More details on the scripts are available in the documentation.
Anima scripts v3.0
Major release of Anima and Anima scripts: more docs and a website are coming to town !
Anima scripts is a set of scripts that use Anima to perform complex preprocessing and core processing tasks on medical images. This repository is multi-platform for most scripts (as long as python is available for your system), except for atlasing scripts that require an OAR scheduler. If you are using Anima scripts for your research, please take the time to:
- Cite the relevant papers referenced in the documentation
- Add a sentence in your acknowledgments section or in the methods part of your paper referencing the RRID of Anima scripts: RRID:SCR_017072, and the one of Anima : RRID:SCR_017017
- if possible, add the link to Anima website: https://anima.irisa.fr
This new release contains the following updates:
- Documentation has moved to read-the-docs for an easier to read version.
- New general website for Anima and Anima scripts available
- Requires Anima v4.0 or higher
- Atlasing scripts now produce all their main results in a residualDir folder and better support input file extensions
- Updated atlas for brain extraction in additional data
- Minor bug corrections in diffusion and relaxometry scripts
More details on the scripts are available in the documentation.
Anima scripts v2.2
Minor update release of Anima scripts, a set of scripts that use Anima to perform complex preprocessing and core processing tasks on medical images. This repository is multi-platform for most scripts (as long as python is available for your system), except for atlasing scripts that require an OAR scheduler. If you are using Anima scripts for your research, please take the time to:
- Cite the relevant papers referenced in the other pages of this documentation wiki or in Anima
- Add a sentence in your acknowledgments section or in the methods part of your paper referencing the RRID of Anima scripts: RRID:SCR_017072, and the one of Anima : RRID:SCR_017017.
This new release contains the following updates:
- Requires Anima v3.4 or higher
- New multi atlas segmentation script on an OAR cluster
- New T2 relaxometry processing script for mono T2 and myelin water fraction estimation
- Other minor bug corrections
More details on the scripts are available on the documentation wiki.
Anima scripts v2.1
Minor update release of Anima scripts, a set of scripts that use Anima to perform complex preprocessing and core processing tasks on medical images. This repository is multi-platform for most scripts (as long as python is available for your system), except for atlasing scripts that require an OAR scheduler. If you are using Anima scripts for your research, please take the time to:
- Cite the relevant papers referenced in the other pages of this documentation wiki or in Anima
- Add a sentence in your acknowledgments section or in the methods part of your paper referencing the RRID of Anima scripts: RRID:SCR_017072, and/or the one of Anima : RRID:SCR_017017.
This new release contains the following updates:
- Requires Anima v3.2 or higher (the 3.3 version is recommended)
- Bug corrections in longitudinal atlas creation
- Online atlasing following the method presented in Legouhy et al. Miccai 2019 paper
- New additional data repository structure, should not change much for this release, but we have switched our additional data to github as well here. A release of additional data has been made as well with this release.
More details on the scripts are available on the documentation wiki.
Anima scripts v2.0
Major update release of Anima scripts, a set of scripts that use Anima to perform complex preprocessing and core processing tasks on medical images. This repository is multi-platform for most scripts (as long as python is available for your system), except for atlasing scripts that require an OAR scheduler. If you are using Anima scripts for your research, please take the time to:
- Cite the relevant papers referenced in the other pages of this documentation wiki or in Anima
- Add a sentence in your acknowledgments section or in the methods part of your paper referencing the RRID of Anima scripts: RRID:SCR_017072, and/or the one of Anima : RRID:SCR_017017.
This new release contains the following updates:
- Requires Anima v3.2 or higher
- Brain extraction now includes an option to further refine the initial mask
- Atlas creation scripts are now python based
- Longitudinal atlas creation scripts
- Several bug corrections and updates to newer version of Anima
- MS segmentation preparation script (registration, denoising and bias correction for further analysis on a reference)
More details on the scripts are available on the documentation wiki.
Anima scripts v1.0
Initial release of Anima scripts, a set of scripts that use Anima to perform complex preprocessing and core processing tasks on medical images. This repository is multi-platform for most scripts (as long as python is available for your system), except for atlasing scripts that require Linux and an OAR scheduler.
This initial release contains the following scripts:
- Atlas-based brain extraction
- Atlas creation from anatomical or DTI images
- Diffusion images pre-processing and multi-compartment models estimation
More details on the scripts are available on the documentation wiki.