Other useful software: DicomSorter is a command line utility for moving DICOM files into folders sorted by patient name, study id, and series. To use, place the executable somewhere in your path, open a command window, navigate to the folder you wish to sort, and type "DicomSorter". Alternatively, you can run DicomSorter from any location and include the name of the folder you wish to sort, eg, "DicomSorter c:\mydicomdir\"¯.
We have script-based sorter available as well. This script is dependent upon DCMTK, which is freely available for Linux systems. The script will sort based on DICOM tag (0018,1030) (ProtocolName), but may be modified to sort on aribitrary DICOM tag(s). Download dcmsort.sh
MRIConvert now supports Enhanced MR image objects. Try MRIConvert 2.0 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 2.0.6, released November 3, 2013. Revision history
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
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
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.
MRIConvert relies on components of the wxWidgets libraries. If you experience errors about missing libraries when running MRIConvert or mcverter, it is likely that your system does not have the required libraries installed. These will need to be installed separately. For Debian flavors as of Debian 6, the command below will install the required componenets.
aptitude install libwxgtk2.8-0
On Redhat/CentOS, wxWidgets is installed using:
yum install wxGTK
If the above command reports that it cannot find wxGTK, you will need to configure yum to use the rpmforge repository. Instuctions for this action are at http://wiki.centos.org/AdditionalResources/Repositories/RPMForge.
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, wxWidgets 2.8 or later and Boost 1.48.0 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.
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:
1.2.840.10008.1.2 Implicit VR, little endian
1.2.840.10008.1.2.1 Explicit VR, little endian
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.
In order to keep up-to-date with changes, please join the MRIConvert mailing list.
MRIConvert is still in development. Please send bug reports and feature requests to email@example.com. 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).