File Management Utilities, by IDeA Lab at UC Davis

File Management Utilities
=========================

***************** Date of current version: Jan 17 2007 ***********

implemented by:

Evan Fletcher

IDeA Lab
Department of Neurology
 University of California, Davis
Davis, California

contact:
emfletcher@ucdavis.edu

List of applications
====================
chg_hdr
chg_data
transformL3 
IF2Ana
Ana2IF
CopyImageParity
GetImageParity
GetImageVolume
GetBytes 
GetOrient
printVolRange
printVolMean
printVoxDims
printVoxMMs
resizeLattice
resizeVox

General Description 
===================
A toolbox of file management and handling functions for interfile 
and analyze format files.

These tools all run in a linux environment. 

Categories of tools
=================== 

a. image and header file management tools
-----------------------------------------

   chg_hdr --> *convert between analyze and interfile header formats
               *edit fields or create analyze header files 
               *do byte swaps for endian problems of analyze header files

                invoke without arguments to see all the options

   chg_data --> do many image manipulation functions. See the website (below) 
                for (fairly) complete list

                invoke without arguments to see all the options

   transformL3 --> reslice image lattice, reorient image, transform image
                   using parameter file or command-line parameters (rotations, 
                   translations, scaling)

                invoke without arguments to see all the options

   resizeLattice
   resizeVox    --> convenience tools to resize image lattice or voxel dimensions; 
                    output new image having desired parameters
   IF2Ana
   Ana2IF -->   conversion scripts to transform file formats (header and image)

b. Image file convenience access routines
----------------------------------------- 

Applications in this category enable quick command-line access of image
characteristics or parameters. The general syntax is to call an application
and supply arguments of header file name together with appropriate options. 
Image file must also be present.

These applications are also useful in scripting situations, e.g. when combining
several operations on image files that require information about the files.

Example:
 
GetBytes myImage.h01   

returns byte storage (i.e. 1, 2 or 4) of a voxel in the interfile image
"myImage"

All routines print their usage if no arguments are given.

   CopyImageParity
    GetImageParity --> output or copy the Parity Matrix for the image
                      for more info on the parity matrix see the bias
                      correction web page listed at the end:
             
                       
   GetBytes
   GetOrient      --> output the voxel byte storage mode or image orientation

   GetImageVolume --> output volume of voxels in image above threshold or
                      at specified value 
   printVolMean
   printVolRange  --> output statistics about the voxel intensities of an
                      image. See options for use with mask files, etc.

   printVoxMMs
   printVoxDims   --> output voxel millimeter dimensions or sizes of the 
                      voxel lattice. May select individual components or
                      output all data at once

Installation
============
-Get the tar file 
-Copy to /usr/local/bin
-tar xvzf  utilities.tar.gz
-Make sure all applications are executable (chmod 755)

IF you place the package somewhere else, change the "bindir"
variable in IF2Ana and Ana2IF accordingly.

Using the tools 
===============
Most tools are self-explanatory. They print their usage when invoked
using no arguments. 

For more information, please see the utilities page of our web site:

 http://neuroscience.ucdavis.edu/idealab/software/utilities.php

for parity matrix information:

http://neuroscience.ucdavis.edu/idealab/software/bias_correction.php#parity.php