catnap_logo_newCATNAP

(Coregistration, Adjustment, and Tensor-solving, a Nicely Automated Program)

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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.

 

Status: Public Release. Downloading constitutes acceptance of this license. Please download and retain for your records.

Platform: Matlab 7 (requires Signal Processing Toolbox)

Contact person: Bennett Landman

Mailing List/User Discussion Pages: CATNAP DTI Google Group

 

9/13/07: SPECIAL NOTE: A video tutorial for using CATNAP. [HTML]

8/16/07: SPECIAL NOTE: New tutorial on batch processing with CATNAP. [HTML]

 

Additional Information       

FAQ (Citing CATNAP)

CATNAP Tutorial 1.0  (Special thanks to Dan Peterson!)

CATNAP Manual 1.0 (VMWare package) (NEW) [HTML] [PDF]

Screen shots

History of the CATNAP Logo

JAVA Source Code for dtiproc (Advanced Users Only: Not Supported Outside of CATNAP)

RESTORE tensor estimation powered by CAMINO

 

Download: 

For Johns Hopkins and Kennedy Krieger Users on Godzilla or Kaiju:

            Instructions_CATNAP_godzilla_users_v1_1.doc (updated 8/27/06)

            Instructions_CATNAP_kaiju_users_v1_0.doc

 

Public Current Release:

Release 3.21 (released 4/20/2008)

·         Removed: Preliminary release of CAMINO 2-tensor fitting

·                                      (still too buggy for public release)

·         Added support to override structural orientations to axial.

·         jfarrell introduced savePARRECavw_forceAnatom2Axial.m

·         (internal release) v3.20 March 17, 2008

·         Preliminary release of CAMINO 2-tensor fitting.

·         Added option to scale structural images.

·         Added option to perform no motion correction (slow).

·         Fixed a long standing problem with multi-echo structural scans

·         where additional echos were "lost" during registration.

            Installation Instructions (CATNAP_installation_v1_0.doc)

User Manual (CATNAP_manual_v1_0.pdf)

Batch Processing Tutorial

 

Prior Releases

 

Publications about CATNAP:

 

Bennett A. Landman, Jonathan A. D. Farrell, Nera-Lee Patel, Susumu Mori, and Jerry L. Prince, DTI Fiber Tracking: The Importance of Adjusting DTI Gradient Tables for Motion Correction. CATNAP – A Tool to Simplify and Accelerate DTI Analysis, Organization for Human Brain Mapping, Chicago, Illinois, June 2007

 

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

 

 

Publications using CATNAP:

Please let us know if you have found CATNAP to be helpful and let us see the interesting work you are doing.

 

J. A. Farrell, B. A. Landman, C. K. Jones, S. A. Smith, J. L. Prince, P. C. van Zijl, and S. Mori. “Effects of SNR on the Accuracy and Reproducibility of DTI-derived Fractional Anisotropy, Mean Diffusivity, and Principal Eigenvector Measurements at 1.5T”, Journal of Magnetic Resonance Imaging. 26(3): 756-767. August 2007.

 

B. A. Landman, J. A. Farrell, C. K. Jones, S. A. Smith, J. L. Prince, P. C. van Zijl, and S. Mori. “Effects of Diffusion Weighting Schemes on the Reproducibility of DTI-derived Fractional Anisotropy, Mean Diffusivity, and Principal Eigenvector Measurements at 1.5T”, NeuroImage. 36(4): 1123-1138. July 2007.

 

Bennett A. Landman, Annie X. Du, Wade D. Mayes, Jerry L. Prince, and Sarah H. Ying, Diffusion Tensor Imaging Enables Robust Mapping of the Deep Cerebellar Nuclei, Organization for Human Brain Mapping, Chicago, Illinois, June 2007

 

Annie X. Du, Bennett A. Landman, David S. Zee, Jerry L. Prince, and Sarah H. Ying, Diffusion Tensor Imaging Reveals Disease-Specific Dentate Nucleus Changes in Cerebellar Degeneration, Organization for Human Brain Mapping, Chicago, Illinois, June 2007

 

B. A. Landman, S. Mori, and J. L. Prince, Systematic Evaluation of Linear and Nonlinear DTI Estimation Methods: An Open Framework, International Society for Magnetic Resonance in Medicine, Berlin, Germany, May 2007

 

B. A. Landman, J. A. Farrell, S. Mori, P. C. van Zijl, and J. L. Prince, Tradeoffs Between Tensor Orientation and Anisotropy in DTI: Impact of Diffusion Weighting Scheme, International Society for Magnetic Resonance in Medicine, Berlin, Germany, May 2007

 

Developers:

            Bennett Landman, Jonathan Farrell, Nera-Lee Patel, Craig Jones

            We appreciate comments, suggestions, bug reports or fixes, and integration of new features. Please contact Bennett Landman or Jonathan Farrell.

 

Last Updated: Tuesday, 27-May-2008 11:02:42 EDT

© Copyright 2006, Bennett Landman. All rights reserved.

THIS PAGE HAS BEEN RETIRED. PLEASE SEE MY NEW WEBSITE.

http://masi.vuse.vanderbilt.edu