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BrainVoyager Available Tools Available Plugins EPI distortion correction: COPE plugin

EPI distortion correction: COPE plugin

Cope user interface screenshot

EPI images suffer from geometric distortions due to non-zero off-resonance fields. The COPE plugin estimates and corrects these deformations using a pair of EPI images acquired with opposite phase-encoding directions (either anterior-posterior and posterior-anterior, or left-right and right-left).

If you don't have the current version of COPE installed, download the ZIP file for your operating system below, unpack it, and place the files in your BrainVoyager plugins folder (e.g., User\Documents\BVExtensions\Plugins_64). You can then start COPE from BrainVoyager's Plugins menu and access the manual by going to Plugins > Description Of Plugins and scrolling down to the section for COPE.

The manual can also be found online here

It is recommended to check whether the similarity to the anatomical image improved after undistortion of the EPI image (FMR/DMR). The similarity can for example be calculated via a NCC-kind of calculation in fmr2vmrplugin, or via the Sørensen-Dice coefficient or mutual information (see Python scripts).

Note 12-11-18: Please note that in the plugin is stated that the order of file submission does not matter; however, it turns out that for some datasets, it is better to upload A>>P as the first file and P>>A as the second file (instead of P>>A first). We will also test this for the file submission order of L>>R and R>>L.

Reference:

H. Breman, J.L.J. Mulders, L. Fritz, J.C. Peters, J. Pyles, J. Eck, M. Bastiani, A. Roebroeck, J. Ashburner, and R. Goebel (2020) An image registration-based method for EPI distortion correction based on opposite phase encoding (COPE). In Lecture Notes in Computer Science (forthcoming), 9th International Workshop on Biomedical Image Registration.

Abstract

Download

COPE 1.1.1

Final versions: Windows 64: Mac OS X, Linux

Beta versions (20-12-19): Windows 64, Mac OS X

COPE 1.1

This is a batch version, which makes it possible to correct distortions for several runs for different subjects.

Mac OS X for BrainVoyager 21, Windows 64-bit for BrainVoyager 21

Example batch files: option 0 (estimate vdm), option 1 (apply vdm), option 2 (estimate vdm and apply to same files), option 3 (estimate vdm and apply vdm to any files in same session)

COPEv11 batchfile general format

 

COPE 1.0

Windows 64-bit for BrainVoyager 20.x, Windows 64-bit for BrainVoyager QX, Windows 7 for BrainVoyager QX

Mac OS X for BrainVoyager 20.x (incl. help)

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