File Conversion and Renaming with MRI Convert

Use the MRIConvert program to give data to meaningful names, and convert them to SPM/Analyze format for smoothest operation with Brain Voyager and/or SPM:

MRIConvert is occasionally updated and improved. You can find the latest version of MRIConvert and documentation at  MRIConvert  and at \\Lauterbur\Public\MRIConvert.

The basic operations are Add a study directory, select an output Directory, and Rename the target directories.

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. 

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 (*.ima) 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.