readme

This directory contains various algorithms for image reconstruction and
other inverse problems such as image restoration and image registration.
It also contains code for related applications including MRI pulse design.


--- GETTING STARTED

After installing the toolbox, use matlab's "path" functionality to put
the top level directory in its path (or launch matlab from that directory).
Then run the file 'setup.m' and all the subdirectories will be added to
the path.  You may find it convenient to read setup.m and customize it.

I recommend running and examining some of the files in the example/ directory
or any of the many ..._example.m files around, such as
	emission/eml_osem_example.m

Many example files prompt you to hit enter before continuing, so you and I
can see the output of each stage before proceeding.
To change this behaviour, execute 'prompt run'
(See utilities/prompt.m for help.)

Some of examples may require the binary program "wt" or "op" that are part
of Aspire.  You can also get Aspire for free by following the instructions
on my web pages.  There are also a couple of mex files that you may need -
wtfmex and f3dmex for example.  I distribute these only in linux/mac formats;
see mex directory.

Part of my motivation for creating these files is to accompany a book on
image reconstruction that I am currently writing.  If you have any problems
with these m-files, or any suggestions whatsover, I welcome your input!

---------------------------------------------------------------------------
Jeff Fessler, http://www.eecs.umich.edu/~fessler/
---------------------------------------------------------------------------


--- Subdirectories (in alphabetical order):

align:
	image registration tools

blob:
	SPECT reconstruction with blob basis functions (not recommended)

contrib:
	algorithms contributed by others.  these directories are not added to
	the path by setup.m so the user must modify the path to use them.

contrib/ppcd:
	test routines comparing WLS-CD, WLS-GCD, WLS-PPCD
	(these are mostly for internal UM use)

ct:
	polyenergetic CT routines (beam hardening, dual energy, etc.)

data:
	data for examples

doc:
	see the pdf file within for some introductory documentation.

emission:
	algorithms for Poisson emission tomography PET/SPECT/ Poisson regression

	eml_	emission maximum likelihood
	eql_	emission quadratically penalized likelihood
	epl_	emission penalized likelihood

example:
	example(s) of usage.  there are more examples in other directories too.
	running any of these examples is a good place to start!

fbp:
	filter-backproject reconstruction, including 2D parallel and fan-beam
	and 3D Feldkamp (FDK) cone beam reconstruction

freemat:
	work in progress, towards making the code run with freemat

general:
	some algorithms that work for generic image reconstruction problems

graph:
	graphics routines

mex:
	MEX (matlab executables), including some C99 source code

mri:
	MR image reconstruction

mri-rf:
	MR pulse design tools, including Spectral-spatial pulse design
	for phase precompensatory slice selection.  (more to come)

nufft:
	non-uniform FFT toolbox

penalty:
	functions associated with regularization

systems:
	system matrices and system matrix object classes
	If you are interested in edge-preserving image restoration
	for a shift-invariant blur model with additive gaussian noise,
	then start with systems/Gblur_test.m and example/restore_example.m
	For tomography, consider starting with systems/Gomo2_strip.m, which
	is used in many of the examples.

transmission:
	algorithms for Poisson transmission tomography

	tml_	transmission ML
	tql_	transmission quadratically penalized likelihood
	tpl_	transmission penalized likelihood

utilities:
	useful matlab utilities for image reconstruction algorithms.

wls:
	algorithms associated with the weighted least squares (WLS)
	cost function and penalized versions thereof

	pwls_	penalized weighted least squares
	qpwls_	quadraticaly penalized weighted least squares

Most algorithms also include a test routine...


--- Additional notes:

Raymod Muzic has matlab routines for reading ECAT files available:
	www.nuclear.uhrad.com/comkat
(I have not yet tried them myself.)

There is one known issue with Matlab7.  It can store sparse matrices
only as doubles with is fine, but if you do "S * x", where S is a
sparse matrix and x is a vector of class single, Matlab7 gives an
error message rather than politely upgrading x to a double.
The object Gsparse.m provides a work around for this.
Complain to Matlab loudly that they should fix this annoyance...

Windows users:

Some of the subdirectories of the "systems" directory contain "links"
to m-files in other directories.  (These are created using "ln -s" in
unix.)  These links are also in the .tar file as soft links.  But these
links may not be recognized by Windoze, resulting in various error messages.
They work fine on Mac OSX since that fantastic operating system is unix
"under the hood."  I recommend that you avoid using Windows.
But if you insist, then you will have to figure out how to fix those links
or copy the appropriate m-files into the appropriate directories.

Another problem is that apparently windoze is case insensitive.
I believe I have purged most of the m-files that had capitalized names now.
Nevertheless, at this point it would be better to just go buy a Mac...