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Name
SurfRelax
Byline
Software for surface analysis; Biomedicon/New York University
Description
SurfRelax is a public domain software suite for automated extraction of topologically correct and anatomically accurate cortical surfaces from MR images.

SurfRelax consists of a set of programs and scripts for Unix, Cygwin, and MacOS X that extract the inner and outer cortical surfaces from a T1-weighted MR image of the human brain. The surfaces are guaranteed to be topologically equivalent to a sphere, thereby obviating the need for handle removal. SurfRelax requires no user intervention, although minor manual editing is recommended for optimal results (normally less than 10 minutes per hemisphere).

SurfRelax has several properties that compare favourably with other software packages for surface reconstruction:
- Free software
- The binaries (written in C++ and Tcl/Tk) are in the public domain. The source code will be released once legacy code issues have been resolved (i.e. replacing with GPL code).
- Uses standard public file formats: Analyze file format (SPM/FSL-compatible) for volumes and OOGL OFF binary format for surfaces (see www.geomview.org)
- Combines advantages of volumetric and surface-based methods for surface generation
- Correct topology of output surface guaranteed
- Requires little or no user intervention - no need for manual handle removal
- Relatively robust to noise - multi-scale method compensates for partial volume effects and intensity inhomogeneities
- Relatively fast (an entire brain is segmented, extracted and unfolded in less than 2 hours of CPU time)
- Powerful editing and visualization tools for volumes and surfaces
- Readily extendable - for instance for use with monkey brains or children's brains
- Can be used to visualize functional data from SPM or FSL
- Includes tools for integration with Stanford's VISTASOFT tools for FMRI data analysis (white.stanford.edu)
NIfTI-1 support
NIFTI-1 will be supported in the next release of SurfRelax. The image orientation of Analyze images currently used in SurfRelax is compatible with NIFTI-1, so the current release will read NIFTI-1 dual header files with 348 byte headers correctly, plus SurfRelax already uses the scale factor defined by the NIFTI convention.
Creator
Jonas Larsson
Contact
jonas@cns.nyu.edu
WWW
www.cns.nyu.edu/~jonas/software.html
Availability
Free
How to get
See webpage
Current version
0.99
Current version release date
2004/1/16
Open source
No
License
See requirements below regarding source code.
Available free of charge
Yes
Requirements
Hardware: 500 MB RAM recommended minimum for good performance. Requires Tcl/Tk, Tix, Qt. Some Unix experience necessary for running command-line programs and scripts. Source code currently unavailable due to legacy code licensing issues. Once resolved by replacing non-GPL code, the source code will be in the public domain.
Technical publications
Larsson, Jonas (2001). Imaging vision: functional mapping of intermediate visual processes in man. PhD Thesis. Karolinska Institutet, Stockholm, Sweden. ISBN: 91-7349-090-3
Applications publications
Schluppeck D, Glimcher P, Heeger DJ. (2005) Topographic organization for delayed saccades in human posterior parietal cortex. J Neurophysiol. 94(2):1372-84. Epub 2005 Apr 7.
Silver MA, Ress D, Heeger DJ. (2005) Topographic maps of visual spatial attention in human parietal cortex. J Neurophysiol. 94(2):1358-71. Epub 2005 Apr 7.
Larsson J, Landy MS, Heeger DJ. (2005) Orientation-selective adaptation to first- and second-order patterns in human visual cortex. J Neurophysiol. 2005 Oct 12; [Epub ahead of print]
Other information
Current users include Stanford University, University of California at Berkeley, New York University, Karolinska Institute
Keywords
functional, segmentation, surface analysis, visualization, volume
Platforms
Any X11 platform; Windows under Cygwin, Linux, MacOS, SunOS, UNIX
IATR listing last updated
21 Feb 2006