getting_spm5
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Transcript 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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