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© Research
Publication : Journal of Open Source Software

Reorient: A Web tool for reorienting and cropping MRI data.

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Journal of Open Source Software - 01 Nov 2020

Heuer K, Toro R

Link to DOI – https://doi.org/10.21105/joss.02670

Link to HAL - Pasteur – https://hal.archives-ouvertes.fr/hal-03745180/

Journal of Open Source Software, 5(55), 2670. https: //doi.org/10.21105/joss.02670

Reorient (https://neuroanatomy.github.io/reorient) is an open source Web application for the manual alignment and cropping of MRI nifti volumes in an intuitive way. The MRI data is dragged onto the Web interface and visualised in an interactive stereotaxic viewer. Users can then translate and rotate the brain by simply dragging inside the 3 view planes, and an adjustable selection box allows to define the crop of the image. Users can save the resulting affine matrix, selection box as well as the reoriented and cropped volume. The affine matrix and selection box can be used later within a scripted workflow, able to reproduce the reoriented volume from the original data. Existing rotation matrices can be loaded or appended.

https://joss.theoj.org/papers/10.21105/joss.02670