Page history Edit this page How do I edit this website?
Original MediaWiki page

FijiRelax

The content of this page has not been vetted since shifting away from MediaWiki. If you’d like to help, check out the how to help guide!

Name

FijiRelax

Software

Fiji

Author

Romain Fernandez

Maintainer

Romain Fernandez

Source

on GitHub

Status

stable, active

Category

Analysis


FijiRelax is a generic tool for 3D+t MRI analysis and exploration using multi-echo spin-echo sequences. This tools is developed in the context of :

Plugin features

  • Proton density, T1 and T2 maps computation from multi-echo spin-echo sequences (multiple TR and/or TE)
  • Parameters estimation by fitting noise-corrected mono- and biexponential decay models
  • Automatic correction of spatial drift and deformations for long T1 or T2 sequences
  • Exploration of T1/T2 distribution in ROI over time
  • Operable through a GUI, or scriptable for batch processing of large datasets
fijirelax-snap-glob-explorer

Time-lapse exploration of parameters in a plant under drought stress

Dataset for testing purpose

A comprehensive dataset can be found on Zenodo at https://doi.org/10.5281/zenodo.4518730

Installation

The following video guide you throughout the installation process, and take a first tour of FijiRelax functions.

In order to install FijiRelax on your computer, please follow these steps:

1. *(if needed) *Download and install Fiji from https://fiji.sc/ ; start Fiji, and let it automatically update. Then restart Fiji.

2. Open Fiji, run the Update manager HelpUpdate. Click on “OK” to close the first popup windows, then click on the button Manage update sites….

3. 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.

4. 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.

5. Restart Fiji: a new FijiRelax entry should be available in the menu PluginsAnalyze. If not, go back to the Update Manager, and check that the repositories ImageJ-ITK and Fijiyama are correctly selected.

Preparing your data

FijiRleax needs properly formatted dataset:

  • Nifti 4D images, or a set of Nifti 3D images
  • Dicom dirs with 3D images, or a set of dirs with 2D images

The interface

FijiRelax interface have four main panels :

  • With the first panel, you can import / open / export data.
  • The second panel holds the processing routines.
  • The third panel contains the explorer button.
  • The fourth panel has additional helper functions.
fijirelax-snap-main-window

FijiRelax main window

Tutorials

Tutorial part 1: proton density, T1 and T2 time-series from 3D dicom data of a sorgho plant

Tutorial part 2: from 4D HyperMaps to time-lapse plant physiology monitoring

HyperMap data structure

The 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 :

  • 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)
  • Channels 4,5, ….. NR-3 are the successive NR repetition times of the “T1 sequence”, in increasing order.
  • Channels NR-2,….. NR-2+NE are the successive NE echo times of the “T2 sequence”, in increasing order.

Unit for the channels 2 and 3 are milliseconds, what mean you can use it like it, without any additional conversion.
For time-lapse experiments, one can compute such a 4D MR hyperimage at successive timepoints, and register and combine them in a 5D MR hyperimage (the same, with an additional slicer to walk through time). Registration and data combining can be done using the series registration mode of the Fijiyama plugin.

The science behind

This plugin compute M0, T1 and T2 maps pixelwise from a given set of spin-echo sequences, acquired with different repetition times and/or different echo times.

First a 3d registration is computed to align precisely the successive images, using libraries of the 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.

Citing this work

  • Romain Fernandez, Cédric Moisy, Christophe Goze-Bac, Maïda Cardoso, Rahima Sidi-Boulenouar, Jean-Luc Verdeil, 2021 «FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t» under review

Software dependencies acknowledgements

  • Johannes Schindelin et al for Fiji (Schindelin et al., 2012)
  • Karl Schmidt for MRI Analysis Calculator and CurveFitters

License

This 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).

This 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.