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 and mcverter
What's New
OS X Lion Support. MRConvert will now
run on OS X Lion with the addtion of the wxWidgets libraries. See below for
a download link.
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 250, released February 1, 2013.
Revision history
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_2.0_r<n>
sh install.sh
where <other stuff> refers to the distribution, version
and release number, and <n> is the release 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. 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 2.6 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:
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.
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@ithelp.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).
