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\”.
MRIConvert
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 revision is 131, dated 12/10/2007. Revision history
To install MRIConvert under Windows, download the zip archive containing the executable and associated text files (MRIConvert_2.0.zip) and unzip them to any directory. The latest archive includes a command line version (mcverter.exe).
Linux users currently have three options: linux binaries (MRIConvert_2.0_linux.zip), the above windows binaries and an emulator such as wine, or building from source. The latest binaries link statically to the wxWidgets libraries, which should solve at least some of the dependency problems many people were having. This version also includes the command line utility, mcverter. To build from source, follow the instructions on the LCNI wiki for building MRIConvert in Ubuntu linux, but get the source code here: mriconvert_sources.zip.
In order to keep up-to-date with changes, please join the MRIConvert mailing list.
MRIConvert is a medical image file conversion utility that converts DICOM files to NIfTI 1.1, Analyze 7.5 , SPM99/Analyze, BrainVoyager, and MetaImage volume formats. More information on how MRIConvert interprets these formats may be found here . It runs on Windows 2k, Windows 98, and Windows XP. MRIConvert was written using wxWindows, an open-source library for cross-platform GUI development.
MRIConvert in action
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.
Three output formats are supported: SPM/Analyze, MetaImage, 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). (MRIConvert version 1.0.2 has the option to save only the *.mhd file.) 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 is still in development. Please send bug reports and feature requests to jolinda@uoregon.edu. 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).
