MRIcron Installation Page

| MRIcron Installation

Introduction

MRIcron can run on Windows, Macintosh OSX and Linux computers. Because Macintosh and Linux builds require a beta-release compiler, installation on these operating systems may be somewhat tricky. This software is covered under a variation of the BSD license. In theory, this software should work well on any of these platforms with recent hardware. However, currently Windows offers the optimal platform for four reasons:

- Graphics are more fluid in the Windows version: uses direct Windows API routines.
- Rendering is faster with the Windows version if you are using a multi-CPU system: Windows version multi-threads rendering, so rendering is twice as fast on a dual-core system.
- Windows version recognizes tablets, making it easier to draw volumes of interest (as it can detect stylus pressure, and can detect whether you are using the stylus tip or eraser).
- Windows version is the most popular, so it has received the most testing from users.

Hopefully, MRIcron should offer reasonable performance on any modern machine. There are a few ways to increase the performance of MRIcron, though these techniques necessarily reduce the quality of the images.

- In the main MRIcron window, make sure that the option '2D smooth all' in the 'View' menu is unchecked. This displays images with the rapid nearest-neighbor interpolation instead of the much slower bilinear interpolation.
- In the rendering window, make sure that the option 'Precise interpolation' in the 'View' menu is unchecked. This generates 3D renderings using nearest-neighbor interpolation instead of the slower trilinear interpolation. Renderings are typically three times faster.
- In the rendering window, you may want to turn off the 'Smooth background' option in the 'View' menu. This displays the raw rendering, instead of applying a 2D blur to the image. Note that this change has much less influence on rendering times than the 'precise interpolation' option (as the precise interpolation is done in all 3 dimensions, while the smooth is only computed in 2 dimensions).

License Chris Rorden's MRIcron, copyright 2007, all rights reserved. Redistribution and use in binary forms, with or without modification, are permitted provided inclusion of the copyright notice, this list of conditions and the following disclaimer is provided with the distribution. Neither the name of the copyright owner nor the name of this project (MRIcron) may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Windows

1. Download the installer.
2. Unzip and run the installer (double click on the .zip file and run the program InstallMR.exe).
3. By default, the installer places the programs in C:\program files\mricron, simply double click on mricron.exe to run the software.
4. You may also double-click on the .bat files, which load example images, for example 'examplefmri.bat' shows two statistical maps on top of a high resolution anatomical scan.
5. Note: The file dcm2nii.exe is compressed using UPX, which can lead some virus software to generate false alarms (AntiVir PE Premium). This software is generated on a computer that always has the latest update's for Trend Micro's OfficeScan virus detection software.

Linux x86 32bit If anyone finds an easier way to distribute this software for Linux, please contact me. I am still finding it tricky to develop a universal protocol for dealing with the dependencies of different distributions.
NoteThe Linux-native version of MRIcron was created using a beta release compiler. In many cases the best solution is to run the Windows-native version of MRIcron using Wine or a virtualized Windows environment (e.g. VMware player, QEMU or Xen).

1. Download the software.
2. Unzip the software (for modern Linux systems, right click on the file mricronlx.zip and choose to 'extract here').
3. Open a terminal window.
4. Change to the folder where you installed mricron, e.g. cd ~/mricron
5. Launch mricron by typing ./mricron (note you must be in the same folder as the mricron executable.
6. You can also run the example .bat files, for example ./xfmri.bat shows two statistical maps on top of a high resolution anatomical scan.

1. In case you receive error messages, check if all the dependencies of the program are installed. In particular, you need

1. GTK 1.2 (this is called GTK+ by some distributions, and gtk by others)
2. libgdk_lixbuf2.0

2. You can see a complete list of .so files needed by the software using the command:
   ldd ./mricron
3. In case you cannot run the program and it displays a message saying it cannot find one of these libraries (you must run the program from the command line to see error messages), you need to download and install a package for the necessary library:
   - On RPM-based distributions you can find packages here: http://rpm.pbone.net/
   - On Debian-based distributions you can find packages here: http://www.debian.org/distrib/packages

Macintosh PowerPC
NoteThe Macintosh:PPC -native version of MRIcron was created using a beta release compiler. In many cases the best solution is to run the Windows-native version of MRIcron using VirtualPC.

1. Download the software.
2. Unzip the software (double click on the .zip file - a new folder called mricron will be created).
3. You will need to install X11.

1. Check to see if X11 is in the applications\utilities folder.
2. If X11 is not installed:

1. OSX 10.4 user can install X11 by using the DVD installer disk
2. Alternatively, download and run the X11 installer distributed by Apple.

4. Download and install the correct version of fink for your version of OS X and let it download and install the additional 29 GTK and related packages needed. Here's the required command for my software (all on one line):

- sudo fink install gdk-pixbuf gtk+ gtk+-data gtk+-shlibs gtk-doc-1.2-13 gtkglarea gtk-engines

5. Launch X11 (double click on the X11 icon in the applications\utilitiesfolder).
6. Launch an X11 terminal (from the keyboard, type Apple-N). From the terminal you can do the following

1. Change to the folder where you installed mricron, e.g. cd ~/Documents/mricron
2. Launch mricron by typing ./mricron (note you must be in the same folder as the mricron executable.
3. You can also run the example .bat files, for example ./xfmri.bat shows two statistical maps on top of a high resolution anatomical scan.

Macintosh Intel
NoteThe Macintosh:Intel -native version of MRIcron was created using a beta release compiler. In many cases the best solution is to run the Windows-native version of MRIcron using VMware Fusion or Parallels Desktop for Mac. .

1. Download the software.
2. Unzip the software (double click on the .zip file - a new folder called mricron will be created).
3. You will need to install X11.

1. Check to see if X11 is in the applications\utilities folder.
2. If X11 is not installed:

1. OSX 10.4 user can install X11 by using the DVD installer disk
2. Alternatively, download and run the X11 installer distributed by Apple.

4. Download and install the correct version of fink for your version of OS X and let it download and install the additional 29 GTK and related packages needed. Here's the required command for my software (all on one line):

- sudo fink install gdk-pixbuf gtk+ gtk+-data gtk+-shlibs gtk-doc-1.2-13 gtkglarea gtk-engines

5. Launch X11 (double click on the X11 icon in the applications\utilitiesfolder).
6. Launch an X11 terminal (from the keyboard, type Apple-N). From the terminal you can do the following

1. Change to the folder where you installed mricron, e.g. cd ~/Documents/mricron
2. Launch mricron by typing ./mricron (note you must be in the same folder as the mricron executable.
3. You can also run the example .bat files, for example ./xfmri.bat shows two statistical maps on top of a high resolution anatomical scan.

Linux x86 64bit While the x86-32bit version may run, in theory it should be possible to create a 64-bit native version by recompiling the source code.
NoteThe Linux-native version of MRIcron was created using a beta release compiler. In many cases the best solution is to run the Windows-native version of MRIcron using Wine or a virtualized Windows environment (e.g. VMware player, QEMU or Xen).

1. Install the compiler. To compile this software, you will need a build of Lazarus created on or after May 1, 2006. This software requires some recent patches that are not available on the current stable release. To get the latest developmental snapshot of Lazarus, click here.
2. Get the source code. The source code is available here. The source file includes sample images in the Templates and Example folders. To test this software, compile mricron.lpr. Next use the File/templates menu to open sample images. Alternatively, after compiling the software, you can click on the included .bat files to see sample renderings.
3. Linux users:You need to have write access to the folder where you run MRIcron (it will want to create .ini files) I suggest placing this software in your home directory.