NRIA 1.0.6

NRIA is New Region of Interest Analysis.

NRIA is a medical image processing program developed at the Brain Behavior Laboratory (BBL) of the University of Pennsylvania; it specializes in the quantitative analysis of PET and MRI images of the brain. The perpetrators are listed in the Credits file.

Despite a nearly total lack of user documentation, NRIA is used heavily at BBL and has been carried by ex-students to infect a few other universities. The only known way to learn how to use the program (unless you wrote it yourself) is to get hands-on training by someone else who already knows how to use it.

NRIA currently runs under Solaris (aka SunOS 5 or greater). A port to any other platform is unlikely, due to the prevalence of non-portable constructs in the code. NRIA will compile but not run successfully using gcc on Linux/Intel; no one is known to have tried it on Linux/Sparc.

Bug reports may be sent to Paul Hughett (hughett@bbl.psycha.upenn.edu), who will add them to his collection. Bug fixes and other improvements may be sent to the same person; context diffs are the preferred format. Should you want to make a more substantial contribution, read the file CodingStyle.

If you still want to install NRIA, see the INSTALL file for instructions. The COPYING file describes the license terms under which the software is made available.

Installation:

These instructions assume that you will put the source tree (where the program is compiled) in a directory /usr/local/src/nria and the executable programs and shared data in a directory /usr/local/nria; if you place them elsewhere, make the appropriate modifications to these instructions.

1. Unpack the source tree with the commands

cd /usr/local/src
gunzip nria-1.0.6.src.tgz
tar xf nria-1.0.6.src.tar

2. Compile NRIA and its supporting programs with the commands

cd nria-1.0.6
make clean
make all

The compiled executables will be placed in one of the directories arch/Linux/bin, arch/SunOS-4/bin, or arch/SunOS-5/bin, depending on your machine architecture and operating system version. (Note that NRIA will compile but not run successfully on Linux; if you want to really use the program you will need a Sun.)

Compiling the whole thing takes about 20-30 minutes, so you might as well go get a cup of coffee while youre waiting. There are about a thousand or so compiler warnings that havent been fixed yet; ignore them.

3. Install the binaries and man pages by

cp -p arch/SunOS-5/bin/* /usr/local/nria
cp -p man/man1/*.1 /usr/local/man/man1

If this is a new installation, install the shared data by

cp -p nria/share/* /usr/local/nria

If this isnt a new installation, you will need to figure some way of merging the new shared data with any local modifications.

You will probably need to be root to do the installation; on the other hand, you can install them in your personal home directory without being root.

4. Add /usr/local/nria to your path, if not already there:

If you are using csh as your shell, then place the following at the end of your $HOME/.login file:

set path = ($path $NRIA)

If you are using sh, ksh, or bash as your shell, then place the following at the end of your $HOME/.profile file:

PATH=${PATH}:$NRIA
export PATH

5. To run NRIA, re-login or type the above appropriate path commands at your shell prompt, and then type:

nria

If you dont have any .nhdr files in the current directory, you will see an empty file dialog. You will need to change directories to one which holds nria format images (raw *.img file, header *.nhdr file). If you only have raw images, then for each image you will need to use the img2ria program (type "man img2ria" for more details). If you have individual slices in their own files, you will need to concatenate all slices into one raw image file, and then run img2ria. NRIA is designed to work with 3D multi-slice volumes, not individual 2D slices.