aslm Files

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            aslm - a slightly modified asl-module

                    http://aslm.sourceforge.net

                              R E A D M E
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This README gives a brief introduction to the installation and use of
aslm. Full details can be found on the aslm website:
                 http://aslm.sourceforge.net

The release is described in the file Contents.m
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aslm
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The idea of this toolbox is to automatize as many parts of an ASL data 
analysis as possible - but allowing the user to interact as often as he 
requests. Usually, the analysis of MRI data involves a lot of repetitive 
tasks like selecting bunches of files for each subject and operating on 
those files etc.
Fortunenately, SPM has the ability to use batches that allow automatizing
these steps once you decide on your analysis setup. Thus, aslm ties in
with these excellent facilities provided by SPM by introducing an object
orientated approach to analysing ASL data. As this type of data is
closely related to other MRI data like BOLD, structural MRI etc., aslm
involves methods to analyze other kinds of MRI data as well. In fact, it
provides different kinds of objects (MRI, ASL, T1, BOLD, ...) that share
common attributes (so called properties) and tasks (so called methods) in
their analysis. 
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Installation
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This software is a suite of MATLAB classes, scripts and data files. 
Portions of the code rely heavily on (or are copied from) SPM8 
(http://www.fil.ion.ucl.ac.uk/spm), 
marsbar (http://marsbar.sourceforge.net), and GIFT (Group ICA of 
fMRI Toolbox v.1.3, http://mialab.mrn.org/software/gift/). The ASL
subtraction-routine is originally from H.Y. Rao & J.J. Wang, @CFN, UPenn
Med, 07/2004, and was modified by A. Federspiel and K. Jann, University 
of Bern.

MATLAB is a commercial engineering mathematics package. 
It is required to use aslm. MATLAB is produced by The
MathWorks, Inc.  Natick, MA, USA. http://www.mathworks.com/ 
<info@mathworks.com.> 
aslm requires only core MATLAB to run (no special toolboxes are required).
 
This software has been written and tested with Matlab 7.11.0.584
(R2010b), SPM8, and marsbar 0.43. It obviously needs SPM8 and marsbar
installed, and GIFT (Group ICA of fMRI Toolbox v.1.3) if you'd like to
use the the additional ICA functionalities.
 
To install aslm, unzip the files in your SPM8/toolbox directory. aslm 
should now be listed in the toolbox menu in SPM8 and can be invoked from 
there. Alternatively, unzip the file where ever you like, change into the
directory containing aslm.m, and type 'aslm('install')' at the command
line. This will try to install aslm into the SPM toolbox directory.

Downloads:
 - Recent distribution of aslm: http://aslm.sourceforge.net/
 - SPM8: http://www.fil.ion.ucl.ac.uk/spm/software/spm8/
 - marsbar: http://marsbar.sourceforge.net/
 - GIFT: http://mialab.mrn.org/software/gift/
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Getting started
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aslm is invoked as toolbox in the SPM8 toolbox menu or with the 
command 'aslm' at the MATLAB prompt. 

Before attempting to analyze data using aslm, please refer to the docu-
mentation provided by SPM8. In addition, there is a user manual avail-
able for aslm on http://aslm.sourceforge.net. 

Like SPM8, aslm uses NIFTI-1 format images as standard.
Consult http://nifti.nimh.nih.gov/dfwg/ for more information.
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Resources
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Please refer to 
 
     http://aslm.sourceforge.net

for a more detailed documentation and a user manual. There is also an 
exemplary data set available that can be downloaded and analysed according 
to the tutorial in the user manual.
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Disclaimer, copyright & licencing
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aslm is free but copyright software, distributed under the
terms of the GNU General Public Licence as published by the Free 
Software Foundation. Further details on "copyleft" can
be found at http://www.gnu.org/copyleft/. In particular, aslm is supplied
as is.  No formal support or maintenance is provided or implied.
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Written by Philipp Homan, University of Bern, Switzerland, 2011-2013
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