This page contains information on common local image analysis issues as well as other relevant information.
Most of the image data and image analysis software tools mentioned here kept on UNIX servers. UNIX is the operation system which manages the computer and allows programs to run. The details of UNIX varies slightly depending on the type of computer on which it is running. The local servers run the GNU/Linux version of UNIX. However, the basic operation of UNIX is fairly generic and there are a wide range of introductions available on-line, including those below. A basic understanding of UNIX will greatly help in the use of the image analysis software.
This is a list of software available on the servers in Radiological &
Imaging Sciences
with links to some instructions and hints. Some programs must be run from
specific computers as noted below. Other programs may be run from all
computers - if you are using a fairly modern PC then consider running the
program locally. If you are using an old and slow PC then first connect to
pmsthes or oberon before running the program. To do this
type ssh -Y username@pmsthes
or ssh -Y username@oberon
(if this command fails, then replace the -Y
with -X
).
avw &
spm
at the Matlab prompt.
spm99
spm2
spm5
fsl33
,
fsl40
, or fsl41
respectively.
fsl &
afni &
jim &
jim4 &
startmricro &
mricron &
dcm2niigui &
imagej &
slicer &
which will run the latest
version. To explicitly run version 3, type slicer3 &
or to
run version 2 type slicer2 &
jmrui &
which will run the latest
version, 4.0. To explicitly run version 3, type jmrui3 &
medinria &
matlab65
matlab
I've written a number of programs for various projects. Instructions of the various options available and a brief overview of how to use the tools are given below. The graphical programs can be compiled to run on most flavours of UNIX including Cygwin. The command line programs are also available to run in a MSDOS command window. The programs are available for use at the University of Nottingham, the MUSC Center for Advanced Imaging Research, and by collaborators. They are not available for general download.
Cygwin is a GNU/Linux-like environment for Microsoft Windows. Cygwin provides a relatively quick and easy solution to give Microsoft Windows desktop users graphical access to the Linux servers. It also allows a few image analysis packages to be run on the local computer rather than on the server, which may speed up certain processing tasks especially if the desktop PC is fairly new. In addition to the wide range of on-line installation and configuration guides, below is a page which describes issues that have arisen locally.