CATNAP

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

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User Manual

 

CATNAP VMWare Distribution

 

Release 1.0

 

Installed Software

CATNAP Release 3.14b

FSL 3.3

Fedora Core 6

Java 1.6

AFNI 2007_05_29_1644

Matlab R2007a (must provide your own license)

 

 

June 21, 2007������������� Initial release for CATNAP Release 3.14b. (BL)

Step 1. Start the CATNAP Virtual Machine with VMWare Viewer. Log in as user �catnap� with the password �catnap�

 

 

Step 2. Start a terminal by clicking on the screen icon along the top of the window.

�

Step 3. Start Matlab by typing �matlab &�

 

 

Step 4.� Start catnap by typing CATNAP in Matlab.

 

Step 5.� Click �Add DWI File�� and select the sample �.par� files in the �Sample Data� folder

 

 

Step 6.� Click �select output path� and select the �processed � folder within the SampleData folder.

 

Step 7. Change the scanner type to �3.0� and select the �Philips No Overplus Low� table.

 

 

Step 8: Click �Select .m File�� and select an m file to create for scripting.

 

Step 9. Click �Generate Processing Script�

 

 

Step 10. Go to the Matlab window. Change the directory to the same directory as your script file. Run the m file by typing the name of the m file (without �.m�) and press enter.

 

Step 12. After processing is complete, you may view the images in MIPAV (type �mipav &� in a terminal) or in Matlab.

Step 13: In Mipav, the dti contrasts may be opened as RAW files (256x256x65 at 0.828125x0.828125x2.2 mm).

The following are little endian floating point: FA, ADC, DXX, DXY, DXZ, DYY, DYZ, DZZ, MB0, MDW, eval1, eval2, eval3.

The following are little endian floating point vector: VEC (not easily ready in MIPAV)

The following is ARGB file: CMAP

Be sure to set the image orientation for proper 3D view:

Example of triplanar view in MIPAV:

�         Fiber tracking may be done with the FA and VEC files on a Windows Platform. The FSL fiber tracking software is included, but not supported by the CATNAP developers. �

�         The virtual machine defaults with 256 MB of RAM. You may increase the settings to improve performance.

�         The root password is �password�.

�         The SampleData are available in already processed form in CATNAP_complete.tar.gz in the SampleData folder.

�         If you expose your virtual machine to the network, be sure to change both the user and root passwords.

�         To process data, we recommend keeping the data on the host computer and using the �shared folders� feature of VMWare to access the data. (The virtual machine�s hard drive is limited to 16 GB total.)

Software Manifest

VMWare 6.0 for Windows Vista

����� http://www.vmware.com/download (Workstation available with 30 trial. Player is free.)

Create a new �linux kernel 2.6.x� virtual machine with 16 GB hard disk and 256 MB RAM.��������

Redhat Fedora Code 6

����� https://www.redhat.com/apps/download/ (SELinux disabled)

Install with �development� package options.�

Use yum to include: �xorg-x11-deprecated-libs� �emacs� �htop� �nedit�

Rpm to install openmotif: http://rpm.pbone.net/index.php3/stat/3/srodzaj/1/search/openmotif

Matlab R2007a & Signal Processing Toolbox

����� http://www.mathworks.com/ (Contact your sales representative.)

AIR 5.2.5

http://bishopw.loni.ucla.edu/AIR5/config.html���������

CATNAP 3.14b

����� http://www.iacl.ece.jhu.edu/~bennett/catnap/catnap.shtml

AFNI (linux xorg7 2007_05_29_1644)

http://afni.nimh.nih.gov/afni/download/afni/releases/latest

FSL 3.3 (source)

����� http://www.fmrib.ox.ac.uk/fsldownloads/main.html

Java 1.6

����� http://www.java.com/en/download/index.jsp

Follow installation instructions. Add all binaries to .bashrc path. Edit CATNAP_defaults.m to set the AFNI path.