Brain Innovation

EPI distortion correction: COPE plugin

Summary

EPI images suffer from geometric distortions due to the susceptibility artifact. The COPE plugin estimates and corrects these deformations using a pair of EPI images acquired with opposite/reverse phase-encoding directions (either anterior-posterior and posterior-anterior, or left-right and right-left).

Installation

To install the most recent version of COPE, download the ZIP file for the operating system below, unpack and place the *.dll/dylib/so, *.js and *.ui files in the BrainVoyager plugins folder (e.g., for the newest BrainVoyager versions: /User/Documents/BrainVoyager/Extensions/Plugins/ and for older versions like BrainVoyager 21.4: /User/Documents/BVExtensions/Plugins_64/).

Usage

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. 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).

Notes

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.

Note 09-12-22: Due to an update of FMR file version 7 (from 'ResolutionX' and 'ResolutionY' to 'NrOfColumns' and 'NrOfRows') in BrainVoyager 22.4.2, COPE might not work as required (update to follow soon). FMR files can be edited with text editors like Notepad (Windows) and TextEdit (macOS).

Note 18-04-24: Due to an update of FMR file version 7 (an added line 'MultibandFactor') in BrainVoyager 23.2.0, BrainVoyager might overlook slice timing information on undistorted files. Update to follow soon. FMR files can be edited with text editors like Notepad (Windows) and TextEdit (macOS).

Downloads

COPE 1.2.2

Change: Plugin with QML script for BrainVoyager 23.

(01-12-23): 1.2.2.1 beta version for macOS (M2): fixing an issue reading batch files, in test phase.

(14-10-23): 1.2.2 for Windows 10/11 from official BV 23 version

(22-04-24): 1.2.2.2 for Windows 10/11 beta version

COPE 1.2.1

Change: accept modified FMR and DMR v7 format (from 'ResolutionX' and 'ResolutionY' to 'NrOfColumns' and 'NrOfRows') from BrainVoyager 22.4.2.

(09-12-22): macOS Windows 64-bit for BrainVoyager 22.4.2; also works for previous versions (checked with BrainVoyager 21.4).

COPE 1.2

Changes: include past transformation information from imported NIfTI files in FMR/DMR, fix display of Help tab.

Beta version (06-05-22): macOS

COPE 1.1.1

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

COPE 1.1

Changes: 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)

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)

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 12120, pp. 122-130, 9th International Workshop on Biomedical Image Registration.

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