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SPM5 Tutorials by the Wellcome Department of Imaging Neuroscience

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1 SPM5 Tutorials by the Wellcome Department of Imaging Neuroscience
SPM5 is all around! SPM5 Tutorials by the Wellcome Department of Imaging Neuroscience

2 SPM5: What’s New? Version Control System: Subversion
me User Interface + Documentation Data Formats (NIFTI-1) Spatial Normalisation and Segmentation fMRI:  Bayesian Analysis with Spatial Priors EEG/MEG:  Time-frequency Analysis  DCM for ERPs  Source Localisation John Will Stefan Jérémie

3 SPM5 SPM5 requirements: Matlab 6.5.1 or 7.0 SPM5 is:
Provided with compiled MEX-files for Windows, Linux (32/64-bit), Solaris. NIFTI-1 file format for images SPM5 is:  500 Matlab files  lines of Matlab code  lines of C code gallons of beer

4 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

5 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 t SPM2 SPM5b SPM5 A fully patched SPM5b is indeed SPM5.

6 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

7 Download SPM5 from the web
Download the latest package:  Registration form:  FTP link where you can download spm5b.tar.gz  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:  Unpack Updates_???.tar.gz to overwrite your SPM installation Updates_README.txt Updates_???.tar.gz Check for updates regularly for new features/bugs fixes…

8 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!

9 Subversion
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).

10 Subversion Repository
SPM repository your SPM working copy SPM Command line Tortoise SVN SPM Update Client interface Subversion library Internet/Intranet (any TCP/IP Network) Subversion server Subversion Repository

11 TortoiseSVN
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.

12 TortoiseSVN: Checkout
URL of the repository: svn:// Right click in the Windows Explorer

13 TortoiseSVN: Update Case 1: your SPM files needed to be updated.
Case 2: your SPM files are up-to-date.

14 TortoiseSVN: Diff If you modify a file:

15 SPM Update Toolbox (1)
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.

16 SPM Update Toolbox (2)  Download the toolbox from:
 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!

17 SPM Update Toolbox (3) Case 1: Your version is up-to-date.

18 SPM Update Toolbox (4) Case 2: Your version is not up-to-date
or you modified some files.

19 Matlab Path Add Folder (and not with Subfolders)
Remove older SPM versions from the path

20 SPM Matlab Files Syntax Definition H1 Line Help Maintainer(s)
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 :58:37Z karl $ H1 Line >> lookfor reml Help >> help spm_reml Maintainer(s) SVN Properties

21 SVN Revision Numbers Each revision number ($Rev$) corresponds to a “snapshot” of the repository: Rev  SPM5b Rev  HEAD (current version) Rev. xxx  SPM5 Differences between the several ways to get SPM: 136: SPM5b xxx: SPM5 252: HEAD Download web Get from network Subversion: TortoiseSVN SPM Update Tbx

22 SPM5 ready to use SPM5 is available… SPM5 is stable…
SPM5 is fully functional…

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