Legend

Port status

Note that these status labels refer to the port, which only controls the installation process, and says nothing about the software itself. An alpha port may have installation issues, but the software it installs may be release quality. Likewise, a committed port will likely build and install without issues, while the software it installs could be full of bugs.

If you have issues installing a port, contact the port maintainer. Contact information is in the Port Makefile. For issues with the software itself, contact the author(s).

• Committed: This port has been committed by the FreeBSD ports team, and is part of the standard FreeBSD ports tree.
• Submitted: Submitted to the FreeBSD ports team. Will appear in the ports tree shortly, pending review by the FreeBSD ports team.
• Stable: Well-tested and stable, but not yet submitted for logistical reasons.
• Beta: Fairly well-tested and stable. Only minor changes likely before being committed.
• Alpha: The port is fully functional and free of known problems, but may undergo significant changes before being submitted. Please help us out by installing this port and reporting any installation problems.

Port name suffix

1. -latest: A stable version, newer than the committed version.
2. -devel: The newest version, still under development, generally alpha-quality.
3. -[date]: Old port based on source code from <date>.

Installing Ports

1. Before you can install a port, you have to install the ports system using portsnap or cvs, or from sysinstall. On PC-BSD, it can also be done from the PC-BSD System Manager. (Choose fetch ports). After doing this, many of the ports here (those marked with "committed" status) will already be in your ports tree.
2. To get ports that are not yet committed, or newer versions of the committed ports (i.e. -latest and -devel), you can download the tarball of all the ports trees and manually unpack them, or use the update_jb_ports script to download and insert them into your ports tree automatically. This will overwrite any previous versions of the ports, unless they are first renamed. You can use the remove_mri_ports script to remove MRI ports frameworks from your ports tree.
3. From here on, you can install any of the thousands of ports as follows:

    cd /usr/ports/category/portname nice make install
   	

   It may take a while for some of the bigger programs, so sit back, have a cup of tea, and browse the WEB while you wait.

OPTIONS

Many ports have build options, to allow the user to enable/disable optional components, such as examples, testing suites, etc. The first time a port is built, a dialog box will appear (see the screenshot of the mritools port below) allowing options to be selected or deselected. If you want to bypass this dialog, and build the port with defaults, define BATCH mode:

nice make -DBATCH install

The mritools metaport

Description: Metaport for installing multiple MRI programs with a single command. Just run make install from /usr/ports/science/mritools to install all of your MRI software. ( Type make config to change the selection afterward. ) Run man mritools after installing for further instructions.

Note that many ports display important configuration information following installation, so you may prefer to install them individually the first time around.

WEB: http://www.neuro.mcw.edu/Ports/
Port status: Stable.
Framework: /usr/ports/science/mritools

AFNI

Description: Analysis of Functional NeuroImaging
WEB: http://afni.nimh.nih.gov
Port status: Committed.
Framework: /usr/ports/science/afni
Notes:

The build date and time reported by AFNI (e.g. AFNI_2006_06_30_1332) are *NOT* updated with every revision of the source code, and hence might not change with every port update. This has been a source of confusion for some users. The port version reflects the actual date of the source code used by the port, so don't be surprised if the version reported when you run AFNI is older than the port version.

Please see notes on shared memory.

The afni program abut is renamed afni_abut to resolve a conflict with the unixstat port.

Caret

Description: Volumetric Analysis Tool
WEB: http://brainvis.wustl.edu
Port status: Submitted.
Framework: /usr/ports/science/caret

DTIQuery

Description: DTI Visualization
WEB: http://graphics.stanford.edu/projects/dti/dti-query
Port status: Committed.
Framework: /usr/ports/science/dtiquery

Disk-to-Disk Clone

Description: Quickly clone FreeBSD systems
WEB: http://www.neuro.mcw.edu/Ports/
Port status: Alpha.
Framework: /usr/ports/sysutils/ddclone

Endian

Description: Report endianness of a system.
WEB: http://www.neuro.mcw.edu/Ports/
Port status: Committed.
Framework: /usr/ports/sysutils/endian

FSL

Description: FMRIB Software Library
WEB: http://www.fmrib.ox.ac.uk/fsl/
Port status: Stable.
Framework: /usr/ports/science/fsl

Insight Toolkit

Description: National Library of Medicine Insight Segmentation and Registration Toolkit
WEB: http://www.itk.org
Port status: Committed.
Framework: /usr/ports/science/InsightToolkit

LENS NNS

Description: Light, Efficient Neural Network Simulator
WEB: http://tedlab.mit.edu/~dr/Lens/
Port status: Committed.
Framework: /usr/ports/math/lensnns

Linux FreeSurfer

Description: FreeSurfer Surface Analysis
WEB: http://surfer.nmr.mgh.harvard.edu
Port status: Stable.
Notes: This is the last planned FreeSurfer port based on Linux binaries. The FreeSurfer team has announced that the source code will be released in the near future. The next planned FreeSurfer port will be a FreeBSD native version based on the public source code.
Framework: /usr/ports/science/freesurfer

Linux Matlab 6.5 R13

Description: Mathworks(tm) Matlab (needed to run SPM)
WEB: http://www.mathworks.com
Port status: Submitted.
Framework: /usr/ports/math/Matlab6
Notes: For FreeBSD 4.x/5.x users with older ports snapshots. Requires linux_base-8, which is deprecated. Should function with other linux_base ports, but the Java desktop may not work. Matlab7 is recommended for users with current systems.

We have been running Linux Matlab on FreeBSD for years, and have experienced only very minor issues, such as annoying warning messages at startup, which can be safely ignored. Most of these issues are corrected by the Matlab port. However, it would still be nice to have a native FreeBSD version of Matlab with full company support. If you would like to see direct company support for running Matlab on FreeBSD, contact Mathworks Support. In order for FreeBSD to become an officially supported platform, Mathworks must see sufficient interest from the FreeBSD community to cover the costs of porting and testing.

Linux Matlab 7.3.0 R2006b

Description: Mathworks(tm) Matlab
WEB: http://www.mathworks.com
Port status: Submitted. See PR 110144.
Framework: /usr/ports/math/Matlab7
Notes: Requires linux_base-fc4 and a recent ports snapshot. (Tested with Mar 07 snapshot on FreeBSD 5.4 and 6.1).
Screenshot:

We have been running Linux Matlab on FreeBSD for years, and have experienced only very minor issues, such as annoying warning messages at startup, which can be safely ignored. Most of these issues are corrected by the Matlab port. However, it would still be nice to have a native FreeBSD version of Matlab with full company support. If you would like to see direct company support for running Matlab on FreeBSD, contact Mathworks Support. In order for FreeBSD to become a supported platform, Mathworks must see sufficient interest from the FreeBSD community to cover the cost of porting and testing.

MCW Eject

Description: A friendlier media eject command for FreeBSD
WEB: http://www.neuro.mcw.edu/Ports/
Port status: Committed.
Framework: /usr/ports/sysutils/mcweject

MINC 1.4

Description: Medical Imaging NetCDF
WEB: http://www.bic.mni.mcgill.ca/software/minc/
Port status: Committed.
Framework: /usr/ports/science/minc

MINC 2.0

Description: Medical Imaging NetCDF
WEB: http://www.bic.mni.mcgill.ca/software/minc/
Port status: Committed.
Framework: /usr/ports/science/minc2

NIFTI C libraries

Description: Neuroimaging Informatics Technology Initiative data format library and tools.
WEB: http://nifti.nimh.nih.gov/
Port status: Committed.
Framework: /usr/ports/science/nifticlib
Notes: Currently, most neuroimaging tools build their own nifti libraries, and often use different versions, which limits the benefit of NIFTI as a standard data format. With the availability of the NIFTI C, Java, and Matlab libraries as separate entities (available from SourceForge), this will hopefully change in the near future.

The nonmritools metaport

Description: Metaport for installing multiple non-MRI programs that happen to be useful in MRI research. Just run make install from /usr/ports/misc/nonmritools. ( Type make config to change the selection afterward. ) Run man nonmritools after installing for further instructions.

Note that many ports display important configuration information following installation, so you may prefer to install them individually the first time around.

WEB: http://www.neuro.mcw.edu/Ports/
Port status: Stable.
Framework: /usr/ports/misc/nonmritools

Praat

Description: Praat Phonetics by Computer
WEB: http://www.fon.hum.uva.nl/praat/
Port status: Committed.
Framework: /usr/ports/audio/praat

RAPID

Description: Robust and Accurate Polygon Interference Detection
WEB: http://www.cs.unc.edu/~geom/OBB/OBBT.html
Port status: Committed.
Framework: /usr/ports/science/rapid

VTK5

Description: Visualization Tool Kit
WEB: http://public.kitware.com/VTK/
Port status: Committed.
Framework: /usr/ports/math/vtk5

Other Ports

You may notice that there are other ports installed by the update_jb_ports script. Feel free to try them out, but be aware that these ports are pre-alpha, and unsupported. As they evolve, they will eventually make their way into this list.

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