Download getting_spm5

SPM5 is all around!
SPM5 Tutorials
by the Wellcome Department of Imaging Neuroscience
SPM5: What’s New?
 Version Control System: Subversion
 User Interface + Documentation
 Data Formats (NIFTI-1)
me
John
 Spatial Normalisation and Segmentation
 fMRI:
 Bayesian Analysis with Spatial Priors
 EEG/MEG:
 Time-frequency Analysis
 DCM for ERPs
 Source Localisation
Will
Stefan
Jérémie
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SPM5
SPM5 requirements:
 Matlab 6.5.1 or 7.0
 Provided with compiled MEX-files for Windows,
Linux (32/64-bit), Solaris.
 NIFTI-1 file format for images
SPM5 is:




 500 Matlab files
 100 000 lines of Matlab code
 10 000 lines of C code
gallons of beer
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SPM5: When?
8 Feb 2005: Teasing by Will on the SPM list
4 May 2005: Mouth watering by John on the SPM list
9 May 2005: Beta release of SPM5 (this is SPM5b (revision 136))
18 May 2005: First updates published
…
October 2005: SPM5 Tutorials
November 2005: SPM5 release
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SPM devel, SPM5b or SPM5?
 “SPM devel” per say doesn’t really exist anymore.
 SPM5b (beta) is on the same line of development
than SPM5 (but not SPM2).
SPM5 line of
development
SPM2 line of
development
SPM2
SPM5b SPM5
t
A fully patched SPM5b is indeed SPM5.
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I want SPM5 here and now !
How to get the latest version of SPM5?
 Old-fashioned ways
 Download it from the web
 Get it from the FIL network
 The disruptive innovation “Subversion”
 What is it?
 TortoiseSVN (Windows only)
 SPM Update Toolbox
 A few more comments
 Revision numbers
 Matlab path
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Download SPM5 from the web
 Download the latest package:
 Registration form:
http://www.fil.ion.ucl.ac.uk/spm/software/download.html
 FTP link where you can download spm5b.tar.gz
ftp://ftp.fil.ion.ucl.ac.uk/spm/restricted/xxxxxx/
 Unpack the tar.gz archive using any data
compression software (WinZip, 7-zip, gunzip, …)
(not using “TAR file smart CR/LF conversion” but “Use folder names”)
 Download the updates:
 FTP directory:
ftp://ftp.fil.ion.ucl.ac.uk/spm/spm5b_updates/
Updates_README.txt
Updates_???.tar.gz
 Unpack Updates_???.tar.gz to overwrite your SPM installation
 Check for updates regularly for new features/bugs fixes…
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Get SPM5 from the FIL network
An updated version is available on the
Unix network: /local/spm/spm5b
Copy this folder to overwrite your local copy from time to time…
Don’t use SPM directly over the network!
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Subversion
http://subversion.tigris.org/
http://svnbook.red-bean.com/
 Subversion is the free/open-source version
control system used for SPM code.
 Manages files and directories over time.
 Remember every change even made to
files and directories.
 Allows to recover older version of the
code or examine the history of how your
data changed.
 Collaborative editing and
sharing of data (source code).
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Subversion
SPM
your SPM
working copy
Command
line
Tortoise
SVN
SPM
Update
Client
interface
Subversion
library
Internet/Intranet
(any TCP/IP Network)
Subversion
server
bread.fil.ion.ucl.ac.uk
SPM
SPM
SPM
SPM repository
Subversion Repository
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TortoiseSVN
http://tortoisesvn.sourceforge.net/
 TortoiseSVN is a free open-source client
for the Subversion version control system.
 Extension for the Windows Explorer.
 Icons overlay shows all versioned /
modified files.
 All Subversion commands available from
the explorer context menu.
 available via a simple right click.
 TortoiseSVN requires the administrative
rights on your computer to be installed.
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TortoiseSVN: Checkout
URL of the repository: svn://bread.fil.ion.ucl.ac.uk/spm/trunk/
Right click in the
Windows Explorer
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TortoiseSVN: Update
Case 1: your SPM files needed to be updated.
Case 2: your SPM files are up-to-date.
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TortoiseSVN: Diff
If you modify a file:
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SPM Update Toolbox (1)
http://www.fil.ion.ucl.ac.uk/spm/local/update/
 An all-in-one Matlab toolbox including
standalone Subversion binaries for several
platforms:
 Windows XP
 Linux (32-bit)
 Solaris
 It does not require the administrative rights
on your computer to be installed.
 The graphical user interface provides only
the Subversion commands you need as a
non-developer (update, no commit).
 All your operations are logged in a text file
so that you can track the exact date of
each time you updated your SPM files. 15
SPM Update Toolbox (2)
 Download the toolbox from:
http://www.fil.ion.ucl.ac.uk/spm/local/update/
 Unpack the .zip archive using any data compression software
 In Matlab, modify the path to include this new directory or move into it.
 Type SPM_update at the prompt and return.
Create a new folder for it!
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SPM Update Toolbox (3)
Case 1: Your version is up-to-date.
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SPM Update Toolbox (4)
Case 2: Your version is not up-to-date
or you modified some files.
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Matlab Path
Add Folder (and not with Subfolders)
Remove older SPM versions from the path
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SPM Matlab Files
function [C,h,Ph,F] = spm_reml(YY,X,Q,N,OPT)
% ReML estimation of covariance components from y*y'
% FORMAT [C,h,Ph,F] = spm_reml(YY,X,Q,N,[OPT]);
%
% YY - (m x m) sample covariance matrix Y*Y' {Y = (m x n) data matrix}
% X
- (m x p) design matrix
% Q
- {1 x q} covariance components
% N
- number of samples
%
% OPT = 1 : log-normal hyper-parameterisation
%
% C
- (m x m) estimated errors = h(1)*Q{1} + h(2)*Q{2} + ...
% h
- (q x 1) ReML hyperparameters h
% Ph - (q x q) conditional precision of h [or log(h), if OPT(1)]
%
% F
- [-ve] free energy F = log evidence = p(Y|X,Q) = ReML objective
%
% Performs a Fisher-Scoring ascent on F to find ReML variance parameter
% estimates.
%__________________________________________________________________________
% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
% John Ashburner & Karl Friston
% $Id: spm_reml.m 249 2005-10-05 17:58:37Z karl $
Syntax Definition
H1 Line
>> lookfor reml
Help
>> help spm_reml
Maintainer(s)
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SVN Properties
SVN Revision Numbers
 Each revision number ($Rev$) corresponds to a “snapshot” of the repository:
Rev. 136  SPM5b
Rev. 252  HEAD (current version)
Rev. xxx  SPM5
 Differences between the several ways to get SPM:
Download web
Get from network
Subversion:
TortoiseSVN
SPM Update Tbx
136: SPM5b
252: HEAD
xxx: SPM5
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SPM5 ready to use
SPM5 is available…
SPM5 is stable…
SPM5 is fully functional…
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