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MRIConvert and mcverter

What's New

MRIConvert now supports Enhanced MR image objects. Try MRIConvert for NIfTI output, Analyze 7.5 output, and automatic generation of diffusion gradient files for Siemens Syngo scanners, Philips, and some GE scanners.

The latest version is 2.1.0, released February 5, 2016. Revision history

Introduction

MRIConvert is a medical image file conversion utility that converts DICOM files to NIfTI 1.1, FSL NIfTI, Analyze 7.5 , SPM99/Analyze, BrainVoyager, and MetaImage volume formats. More information on how MRIConvert interprets these formats may be found here

MRIConvert In ActionMRIConvert in action

Installation

Windows - To install MRIConvert under Windows, download MRIConvert-2.1.0-win32.zip and extract the contents to any directory.

OS X - Image of installer download the image MRIConvert-2.1.0.dmg

Linux - If you use a Debian-based distro (e.g. Ubuntu), we highly recommend using the NeuroDebian repository as the Right Way to install MRIConvert. Install by running "aptitude install mriconvert" as the administrative user. Any necessary libraries should be installed automatically.

If you are not yet using NeuroDebian, download one of the binary distributions listed below. Due to differences in typically installed libraries between Redhat and Debian-based distros, we have provided different builds for each. Choose the tarball that most closely matches your Linux flavor:

Installation is accomplished with the following commands:

tar xzf MRIConvert-<other stuff>.tar.gz
cd MRIConvert-<version>
sh install.sh

where <other stuff> refers to the version and distribution, and <version> is the version number. You will need root privileges as the default installation location is /usr/bin.

Other - Finally, you could build from the source code tarball or zip file. If your platform is not listed above, there may be a reasonable chance that MRIConvert can be built natively. You will need a C++ compiler that understands the Standard Template Library and wxWidgets 2.8 or later. Please let us know if you get this working, it would be great to list your platform here.

If none of the above works for your system, email us on the MRIConvert mailing list and we will attempt to provide a working solution.

Basic Usage

To choose files to convert: choose "Input/Add" from the menu, or click on the "Add" button. This will bring up a directory selector dialog. Choose a directory containing the files you wish to convert. All DICOM files in this directory and its subdirectories will be added to the "DICOM input" panel. Files must end in ".dcm" and must conform to the DICOM standard to be included. At the moment, MRIConvert can only convert files that use the following transfer syntaxes:

The input files are organized by subject, study, and series into a tree structure. Subjects, studies, or series that you don't wish to convert may be deleted from the input list by choosing "Input/Remove" from the menu or by clicking on the "Remove" button. Individual files may not be deleted from a series.

Before converting files, the user may view images, DICOM header information, or a summary of information for a series. Individual images may be converted to JPEG, BMP, or TIFF formats. DICOM information may be saved to a text file from the DICOM viewer.

MRIConvert creates a directory structure based on series and subject. Directories and output files are given default names based on subject, study, and series information. The user may change these names by selecting the file or directory to be renamed and choosing "Output/Rename" from the menu or by clicking on the "Rename" button. To change to root directory for output, choose "Output/Directory" from the menu or click on the "Directory" button.

Six output formats are supported: FSL NifTi, SPM Analyze, Meta Image, NifTi, Analyze 7.5 and BrainVoyager. For SPM99/Analyze, two output files are created for each volume: a header file (*.hdr) and an image file (*.img) containing raw data. The image file is in standard analyze coordinates (RAH). Similarly, two output files are created for each MetaImage volume: a text header file (*.mhd) and a volume file of raw data (*.raw). The raw data is in DICOM standard coordinates (LPH). You can select the output image format from the pull-down choice box.

If BrainVoyager output format is chosen, anatomical series will be converted to .vmr files, and functional series will be converted to .fmr and .stc files. Currently, only Siemens mosaic-format files are identified as functional series. For anatomical series, the original data may be saved in a .v16 file by checking the obvious box.

To convert files, choose "Convert/Convert All" from the menu, or click on the "Convert" button.

MRIConvert Mailing List

In order to keep up-to-date with changes, please join the MRIConvert mailing list.

Final Words

MRIConvert is still in development. Please send bug reports and feature requests to . MRIConvert was developed at the Lewis Center for Neuroimaging at the University of Oregon. All LCNI software is available free of charge under the GNU General Public License (GPL).

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