Available plugins

Introduction
Introduction Plugins extend the computational capabilities of BrainVoyager. As ... more
NIfTI conversion plugin

Conversion between BrainVoyager and NIfTI file formats

NIfTI is a file format to save volumetric (f)MRI data and is the successor of Analyze 7.5. NIfTI-BIDS is the successor of NIfTI and supported in BrainVoyager.
 
Just for the few cases where BrainVoyager conversion functions cannot be used, the plugin to import from NIfTI to BrainVoyager formats and from BrainVoyager formats to NIfTI is still available from this support site.
Please note that positioning information of non-native conversions might not be accurate. Import/export of data with native (scanner) positions should be fine. This tool should in no circumstances be used for any medical purposes.
 
 
Versions
 
NIfTI converter 1.09: macOS Intel, Windows 64-bit for BV 21, Linux Ubuntu, manual
 

Conversion options between BrainVoyager and NIfTI

 

Import to 3D statistical map (VMP)

In BrainVoyager 23, a statistical volume map can be loaded on the anatomical image in the 3D Volume Map dialog via the "Load..." button (see Figures below).

 

 

 
 
For specific cases, for example import of statistical volume maps to VMP in non-sagittal orientation, there is for example also a Python script to convert from NIfTI to VMP: please see https://helpdesk.brainvoyager.com/626518-Python-script-to-convert-NIfTI-to-VMP.
 

Workaround for import of unsigned 32-bit integer masks from CONN Toolbox

Problem:

NIfTI format masks with cluster labels (e.g., {0, 1, 2, 3, etc.}) generated from a seed-to-voxel analysis and exported using the "export mask" feature of the CONN MATLAB toolbox.
When opening the NIfTI file in BrainVoyager, an error message was displayed: "data type 768 is currently not supported," which suggested to me that the issue was related to the "variable/data type" that CONN was using to store the data for each voxel.
Although the range of label values was just {0, 1, 2} in this case, CONN was using a datatype with ID 768 (unsigned int 32 bits https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/datatype.html), as confirmed in the NIfTI file header metadata using software like ITKsnap.

Solution that was tested and worked:

Open the NIfTI file using ITKsnap and save it without making any changes. This approach can probably be applied using other NIfTI reading software as well.
ITKsnap seems to adjust the "variable/data type" with which it saves the NIfTI file based on the range of variable values (in this case {0, 1, 2}) and thus saved it using a data type with ID 4 (DT_INT16), which appears to be compatible with BrainVoyager. Make sure to verify that the newly saved image matches the original one and that no data was lost in the process.

Kindly contributed by Ricardo Martins

 
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COPE: EPI distortion correction (image registration-based)

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 (see below for update). 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.

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

(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

 

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).

Example batch files

Batch files for 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) can be found attached to this page.

 

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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