CATNAP
Overview
CATNAP (Coregistration, Adjustment, and Tensor-solving, a Nicely Automated Program) is an end to end data processing pipeline for Philips PAR/REC Magnetic Resonance data files. CATNAP performs motion correction for both diffusion and structural images using FSL FLIRT, adjusts the diffusion gradient directions for scanner settings (i.e., slice angulation, slice orientation, etc.) and motion correction (i.e., the rotational component of the applied transformation), and computes tensor and derived quantities (FA, MD, colormaps, eigenvalues etc) . The results are readily compatible with DTIStudio, FSL, and other tensor analysis packages.
Name
CATNAP (Coregistration, Adjustment, and Tensor-solving, a Nicely Automated Program)
Version Number
3.0
Short Description
CATNAP (Coregistration, Adjustment, and Tensor-solving, a Nicely Automated Program) is an end to end data processing pipeline for Philips PAR/REC Magnetic Resonance diffusion tensor imaging and structural experiments.
Logo
none – The CATNAP logo on http://iacl.ece.jhu.edu/~bennett/catnap/catnap.shtml may be used, but it is not required.
Figure
Categories and Keywords
Diffusion Tensor Imaging; DTI; Philips; PAR/REC; coregistration; gradient table correction; analysis
Longer Overview
CATNAP (Coregistration, Adjustment, and Tensor-solving – a Nicely Automated Program) is an end to end data processing pipeline for Philips PAR/REC Magnetic Resonance data files. CATNAP performs motion correction for both diffusion and structural images using FSL FLIRT, adjusts the diffusion gradient directions for scanner settings (i.e., slice angulation, slice orientation, etc.) and motion correction (i.e., the rotational component of the applied transformation), and computes tensor and derived quantities (FA, MD, colormaps, eigenvalues etc) . The results are readily compatible with DTIStudio, FSL, and other tensor analysis packages.
User Manual
See: http://iacl.ece.jhu.edu/~bennett/catnap/catnap.shtml
Register for Download
See: http://iacl.ece.jhu.edu/cgi-bin/download.scgi?sw=catnap
Installation Information
See documents at: http://iacl.ece.jhu.edu/~bennett/catnap/catnap.shtml
References for the Software
B. A. Landman, J. A. Farrell, S. Mori, P. C. van Zijl, and J. L. Prince, On the Coregistration of Diffusion Weighted Images, International Society for Magnetic Resonance in Medicine, Seattle Washington, May 2006
Acknowledgements to Include
The developers would appreciate an acknowledgement of their many hours of work and continued development time on the CATNAP project. If CATNAP has been useful to your project, saved you time, limited your gray hair, alleviated heartburn and otherwise made DTI processing simple, please cite CATNAP as follows.
Acknowledgement: The CATNAP software was kindly provided by Bennett Landman et al, (Johns Hopkins University) [citation]. The development of this software was supported by NIH/NCRR grant RR15241 to the Kennedy Krieger Institute (PVZ) and the Image Analysis and Communications Laboratory (JP).
CATNAP (Coregistration, Adjustment and Tensor-solving, a Nicely Automated Program) release 2.2 (2006)
Landman BA, Farrell JAD, Jones CK, Patel N, Prince JL
Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
In text reference (Landman et al, 2006)
Contributors/Authors
B. A. Landman
J. A. Farrell
S. Mori
P. C. van Zijl
J. L. Prince
C. Jones
Nera-Lee Patel
Technical Contacts
B. A. Landman, bennett@bme.jhu.edu
J. A. Farrell, jonfarrell@jhu.edu
Acknowledgements of Funding Sources
The development of this software was supported by NIH/NCRR grant RR15241 to the Kennedy Krieger Institute (PVZ) and the Image Analysis and Communications Laboratory (JP).
License
http://iacl.ece.jhu.edu/~bennett/catnap/license.shtml
Binary/Data Distribution
The distribution includes Matlab (text and editable binary ) and binary Java JAR files.
Source Distribution
The source and binary distributions have been tested on Matlab 7 with Solaris, Linux, and Windows.
Source Distribution Instructions
This should be a point-and-click from the portal to CATNAP’s source (.m) file and its installation and user documentation.
Dependencies
Matlab 7 (required)
FSL 3.3 (required)
Cygwin (Windows Only, required)
Screenshots
Main GUI
Tool to automatically rename files based on protocol
Site URL
http://iacl.ece.jhu.edu/~bennett/catnap/catnap.shtml