{"id":20566615,"url":"https://github.com/rocsg/fijirelax","last_synced_at":"2025-10-19T06:49:41.442Z","repository":{"id":60144559,"uuid":"334968337","full_name":"Rocsg/FijiRelax","owner":"Rocsg","description":"FijiRelax: 3D+t multi-echo spin-echo sequences MRI analysis","archived":false,"fork":false,"pushed_at":"2025-04-02T10:45:19.000Z","size":8134,"stargazers_count":8,"open_issues_count":6,"forks_count":4,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-14T14:36:52.547Z","etag":null,"topics":["image-processing","imagej","imagej-plugins","java","modeling","mri","relaxation-time"],"latest_commit_sha":null,"homepage":"https://imagej.net/plugins/fijirelax","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Rocsg.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-02-01T14:02:17.000Z","updated_at":"2025-04-02T10:45:23.000Z","dependencies_parsed_at":"2025-04-14T14:37:00.919Z","dependency_job_id":"d37e0988-21ab-45cb-93a9-15a3443f1ede","html_url":"https://github.com/Rocsg/FijiRelax","commit_stats":{"total_commits":237,"total_committers":4,"mean_commits":59.25,"dds":"0.012658227848101222","last_synced_commit":"38e0abfc5cb4a14dd8b9b8dabc8170ff4ed4e710"},"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Rocsg%2FFijiRelax","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Rocsg%2FFijiRelax/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Rocsg%2FFijiRelax/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Rocsg%2FFijiRelax/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Rocsg","download_url":"https://codeload.github.com/Rocsg/FijiRelax/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248911244,"owners_count":21182060,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["image-processing","imagej","imagej-plugins","java","modeling","mri","relaxation-time"],"created_at":"2024-11-16T04:42:42.046Z","updated_at":"2025-10-19T06:49:41.331Z","avatar_url":"https://github.com/Rocsg.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Documentation and latest stable build\n[![javadoc](https://javadoc.io/badge2/io.github.rocsg/fijirelax/javadoc.svg)](https://javadoc.io/doc/io.github.rocsg/fijirelax)\n[![Maven Central](https://img.shields.io/maven-central/v/io.github.rocsg/fijirelax.svg?label=Maven%20Central)](https://search.maven.org/search?q=g:%22io.github.rocsg%22%20AND%20a:%22fijirelax%22)\n[![DOI](https://joss.theoj.org/papers/10.21105/joss.04981/status.svg)](https://doi.org/10.21105/joss.04981)\n\n## Summary\n\nFijiRelax is a generic tool for 3D+t MRI analysis and exploration using multi-echo spin-echo sequences. This work was supported by the French Ministry of Agriculture, France AgriMer, CNIV and IFV, within VITIMAGE and VITIMAGE-2024 projects (program Plan National Dépérissement du Vignoble). \n\n\n## Funding\nThis tools are developed in the context of:\n- the [Vitimage 1](https://www.plan-deperissement-vigne.fr/recherches/programmes-de-recherche/vitimage) and [Vitimage 2024](https://www.plan-deperissement-vigne.fr/recherches/programmes-de-recherche/vitimage-2024) projects.\n- the [Aplim](https://umr-agap.cirad.fr/recherche/projets-de-recherche/aplim) flagship project. \n\n\n## Plugin features\n\n- Proton density, T1 and T2 maps computation from multi-echo spin-echo sequences (multiple TR and/or TE)\n- Parameters estimation by fitting noise-corrected mono- and biexponential decay models\n- Automatic correction of spatial drift and deformations for long T1 or T2 sequences\n- Exploration of T1/T2 distribution in ROI over time\n- Operable through a GUI, or scriptable for batch processing of large datasets\n\u003cimg src=\"https://github.com/Rocsg/FijiRelax/blob/master/images/fijirelax-snap-glob-explorer.png\" width=\"800\" caption=\"Time-lapse exploration of parameters in a plant under drought stress\"\u003e\n \n\n ## Using FijiRelax, from GUI to API\n \n FijiRelax has been designed for three types of scientists: i) end-users using a GUI, ii) advanced users able to use a scripting languages to process large number of images, and iii) developers able to adapt and extend the application with new functionalities.\n\n* **End-users using a GUI**: this mode is recommended for scientists who are not specialists in image processing nor programming. Download FijiRelax through the official Fiji release, and follow the step-by-step installation instructions, as well as the hands-on tutorials built on the test dataset hosted at Zenodo [@fijirelaxDataset]. Then, use the graphical user interface to import and process your own Bruker/NIFTI/Custom data, explore the relaxation maps in space and time using the graphical relaxation curve explorer and export your results as 2D/3D/4D TIFF images. This mode is also recommended for studying new datasets or new biological questions. Among the interface features, the plugin provides a graphical explorer to visualize the relaxation curves, and the estimated PD-weighted T1 and T2 distributions over customizable areas of interest. In 5D hypermaps, the distributions at each time-point can be displayed simultaneously, giving access to valuable information on water distribution in tissues and its evolution during the monitoring period.\n\n* **Advanced users**: this mode can be used by scientists with programming skills. Load the sample BeanShell scripts provided in repository in https://github.com/Rocsg/FijiRelax/tree/master/test/Scripts. Select a script by dragging it into the Fiji interface and run the scripts to reproduce the results of the paper figure1: import a dataset, convert it to an HyperMap (figure1-e), compute the parameter maps. Then, adapt these scripts to your needs, including processing your own data and batch-processing multiple experiments.\n\n* **Developers**: this mode is for programmers fluent with Java and Maven. Start by exploring the FijiRelax API: [API Overview](https://javadoc.io/doc/io.github.rocsg/fijirelax/latest/index.html). Build your own tools on top of the FijiRelax library, provided as a jar file hosted at maven central repository ([Artifact](https://search.maven.org/artifact/io.github.rocsg/fijirelax)), by indicating FijiRelax as a dependency in your POM file and run the unit tests. FijiRelax is hosted on a github public repository ([https://github.com/rocsg/fijirelax](https://github.com/rocsg/fijirelax)) and developers can offer to contribute to its development, and extend it by requesting features, or proposing new features.\n\n \n## Dataset for testing purpose\n\nA comprehensive dataset can be found on Zenodo at [https://doi.org/10.5281/zenodo.4518730](https://doi.org/10.5281/zenodo.4518730) \n\n\n\n## Installation\n\nThe following video guide you throughout the installation process, and take a first tour of FijiRelax functions.\n\n[![Installation](https://i.ytimg.com/vi/8jEVQjRbFcU/hqdefault.jpg)](https://www.youtube.com/watch/8jEVQjRbFcU)\n\n\nIn order to install FijiRelax on your computer, please follow these steps:\n\n1\\. *(if needed) *Download and install Fiji from https://fiji.sc/ ; start Fiji, and let it automatically update. Then restart Fiji.\n\n2\\. Open Fiji, run the **Update manager** (Help \u003e Update). Click on \"OK\" to close the first popup windows, then click on the button **Manage update sites...**.\n\n3\\. In this list, activate **ImageJ-ITK** by checking the corresponding checkboxes. Don't close the window, or reopen it if you read this too late.\n\n4\\. Add the **Fijiyama** repository (by clicking on the button **Add update site**, and filling the fields : name = \"/plugins/fijiyama\", site = https://sites.imagej.net/Fijiyama), then check the associated checkbox. Now you can click on **Close** and apply the modifications.\n\n5\\. Restart Fiji: a new **FijiRelax** entry should be available in the menu (Plugins \u003e Analyze\"). If not, go back to the Update Manager, and check that the repositories **ImageJ-ITK** and **Fijiyama** are correctly selected.\n\n\n## Preparing your data\n\nFijiRleax needs a properly formatted dataset:\n- Nifti 4D images, or a set of Nifti 3D images\n- Dicom dirs with 3D images, or a set of dirs with 2D images\n\n\n## The interface\n\nFijiRelax's interface has four main panels :\n- With the first panel, you can import / open / export data.\n- The second panel holds the processing routines.\n- The third panel contains the explorer button.\n- The fourth panel has additional helper functions.\n\n\u003cimg src=\"https://github.com/Rocsg/FijiRelax/blob/master/images/fijirelax-snap-main-window.png\" width=\"300\" caption=\"FijiRelax main window\"\u003e\n\n\n \n\n## Tutorials\n\n**Tutorial part 1: proton density, T1 and T2 time-series from 3D dicom data of a sorgho plant**\n\n[![Tutorial part 1](https://i.ytimg.com/vi/nhWRZN9puFg/hqdefault.jpg)](https://www.youtube.com/watch/nhWRZN9puFg)\n\n**Tutorial part 2: from 4D HyperMaps to time-lapse plant physiology monitoring**\n[![Tutorial part 2](https://i.ytimg.com/vi/tiJnq_xN-dY/hqdefault.jpg)](https://www.youtube.com/watch/tiJnq_xN-dY)\n\n## HyperMap data structure\n\nThe output image is a 4D MR hyperimage. The \"channels\" slicer helps you to explore the 4th dimension, that is the images computed, and the input spin echo images. In detail :\n\n-   Channels 1,2 3 are respectively the M0 map, T1 map, T2 map (see this information in the slice title, just upside the image pixels)\n-   Channels 4,5, ..... NR-3 are the successive NR repetition times of the \"T1 sequence\", in increasing order.\n-   Channels NR-2,..... NR-2+NE are the successive NE echo times of the \"T2 sequence\", in increasing order.\n\n  \nUnit for the channels 2 and 3 are milliseconds, which means you can use it like it, without any additional conversion.  \nFor time-lapse experiments, one can compute such a 4D MR hyperimage at successive timepoints, and register and combine them in a 5D MR hyperimage (with an additional slicer to walk through time). Registration and data combining can be done using the series registration mode of the [Fijiyama](/plugins/fijiyama) plugin.\n\n  \n## The science behind\n\nThis plugin computes M0, T1 and T2 maps pixelwise from a given set of spin-echo sequences, acquired with different repetition times and/or different echo times.\n\nFirst a 3d registration is computed to align precisely the successive images, using libraries of the [Fijiyama](/plugins/fijiyama)  plugin. Then the rice noise level is estimated, and the M0, T1 and T2 parameters are estimated, fitting mono or bi-exponential curves, corrected with the measured rice noise. For more information, see the paper in next section.\n\n## Support\nFeature request, issues ? Please post a message on the [the ImageJ forum](https://forum.image.sc/), using the tag `fijirelax` . For precise requests, technical users can use a github issue, or pull-request modifications (see CONTRIBUTE.md)   \n\n \n## Citing this work\n\n- Romain Fernandez and Cédric Moisy, 2022  «FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t» *under review*\n\n## Software dependencies acknowledgements\n\n- Janne Holopainen for LMA\n- Johannes Schindelin et al for [Fiji](/software/fiji) (Schindelin et al., 2012)\n- Karl Schmidt and Dimiter Prodanov for MRI Analysis Calculator and CurveFitters\n\n## License\n\nThe code of FijiRelax is distributed under GPL 2.0 public license and authorship of Romain Fernandez romainfernandez06@gmail.com io.github.rocsg\nIt includes code of Janne Holopainen (LMA), released as GPL 2.0 in the context of this repository\n \n\nThis program is an open-source **free software**: it can be redistributed and/or modified under the terms of the **GNU General Public License** as published by the Free Software Foundation ([http://www.gnu.org/licenses/gpl.txt](http://www.gnu.org/licenses/gpl.txt)).\n\nThis program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frocsg%2Ffijirelax","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frocsg%2Ffijirelax","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frocsg%2Ffijirelax/lists"}