Diff for "SpmInformation" - MRC CBU Imaging Wiki
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= Information on using and tuning SPM = This is a practical guide to using SPM. If you're after theory, you might want the Analysis Principles section from the menu on the left.
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 * [http://www.fil.ion.ucl.ac.uk/spm/ FIL/SPM home page]
 * SpmQuickStart		 = Getting started with SPM =
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 * SpmWithPentium4 - tuning SPM for the Pentium 4 chip
 * [http://gnumex.sourceforge.net/ Compiling SPM on Windows]
 * SpmBenchmarks - benchmarks from machines running SPM
 * SpmBatch - batching SPM jobs
 * [http://www.sph.sc.edu/comd/rorden/mritut.html Normalizing anatomical MRI scans of damaged brains] using SPM and MRIcro.
 * MaskedEpiNormalization - using the EPIs for spatial normalization. 		  * SpmManuals
= SPM tips and tools =
 * [[http://www.sph.sc.edu/comd/rorden/mritut.html|Normalizing anatomical MRI scans of damaged brains]] using SPM and MRIcro.
 * MaskedEpiNormalization - using the EPIs for spatial normalization.
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 * SpmGraphics - using the SPM output graphics for making figures
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 * TrimmingImages using SPM
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 * [http://www-psych.stanford.edu/~kalina/SPM99/ Kalina Christoff's SPM99 page] - a variety of interesting programs, protocols and discussions.
 * SpmManuals
 * The [http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/ Human Brain Function book] - these are a series of chapters covering theory and to some extent implementation in SPM of the areas below. Be warned that some of these chapters are aimed at quite a high level, and may be hard to follow for those without relevant background.
 * [http://www.fil.ion.ucl.ac.uk/spm/dox.html Papers published by the FIL group on SPM] - these are available online via the SPM website, as are some other important papers on related theory.
 * [http://www.fil.ion.ucl.ac.uk/spm/course/ SPM course notes]
 * Rik Henson's CBU SpmMiniCourse2005
 * CBU SpmMiniCourse2007		  * TrimmingImages using SPM
= Automating SPM =
 * [[AA|aa]] - automating SPM analyses
 * SpmBatch - batching SPM jobs
= Programming with SPM =
 * SpmGraphics - using the SPM output graphics for making figures
 * BasicProgrammingWithSpm
= Benchmarking SPM =
 * SpmWithPentium4 - tuning SPM for the Pentium 4 chip
 * [[http://gnumex.sourceforge.net/|Compiling SPM on Windows]]
 * SpmBenchmarks - benchmarks from machines running SPM
 * TestsNewConfigJuly2009 - testing different configurations of Linux with various neuroimaging packages
= Recent Updates =
== 2009/08/25 Default spm 8 to Matlab2009a ==
{{{
spm 8
}}}
now defaults to matlab2009a as this offers the full functionality
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Also, you may do commands like

{{{
spm 5 matlab2009a
}}}
[RC]

== 2008/11/26 Update Juelich's Anatomy toolbox for SPM 5 ==
Obtained a new pre-release version of the toolbox, containing new maps for the parietal lobe. Replaced the old version [RC]

== 2008/10/6 Installed Juelich's Anatomy toolbox into SPM 5 ==
[RC]

== 2008/08/13 Added highmemory switch to spm ==
If you launch spm with {{ spm highmemory }} you will be sent to a machine with 16 GB of RAM.

[RC]

= 2008/02/07 Added function HeadMask.m to /imaging/local/spm/common_spm5andabove =
This function attempts to mask out the vitamin E capsules from T1 weighted structurals. This is useful before producing a scalp mesh, which may otherwise be distorted. It has been tested on seven subjects, never removing anything it shouldn't, and successfully removing the vitamin E capsules in six of the seven cases. (Including one patient with lesions; use at own risk; does NOT seem to improve normalisation to MNI space.)

[DannyMitchell]
== 2008/02/06 Patched spm_getSPM manually ==
Fixed bug when saving design matrix from contrast manager as identified by Catherine Marie-Longtin, and solved by Ferath Kherif

{{{
put
cd(SPM.swd) at line 200,
just after the code : SPM.swd = swd; at line 199.
}}}
[RC]

= Getting more help =

This is a practical guide to using SPM. If you're after theory, you might want the Analysis Principles section from the menu on the left.

Getting started with SPM

SPM tips and tools

Automating SPM

  • aa - automating SPM analyses

  • SpmBatch - batching SPM jobs

Programming with SPM

Benchmarking SPM

Recent Updates

2009/08/25 Default spm 8 to Matlab2009a

spm 8

now defaults to matlab2009a as this offers the full functionality

Also, you may do commands like 

spm 5 matlab2009a

[RC]

2008/11/26 Update Juelich's Anatomy toolbox for SPM 5

Obtained a new pre-release version of the toolbox, containing new maps for the parietal lobe. Replaced the old version [RC]

2008/10/6 Installed Juelich's Anatomy toolbox into SPM 5

[RC]

2008/08/13 Added highmemory switch to spm

If you launch spm with spm highmemory you will be sent to a machine with 16 GB of RAM.

[RC]

2008/02/07 Added function HeadMask.m to /imaging/local/spm/common_spm5andabove

This function attempts to mask out the vitamin E capsules from T1 weighted structurals. This is useful before producing a scalp mesh, which may otherwise be distorted. It has been tested on seven subjects, never removing anything it shouldn't, and successfully removing the vitamin E capsules in six of the seven cases. (Including one patient with lesions; use at own risk; does NOT seem to improve normalisation to MNI space.)

[DannyMitchell]

2008/02/06 Patched spm_getSPM manually

Fixed bug when saving design matrix from contrast manager as identified by Catherine Marie-Longtin, and solved by Ferath Kherif 

put
cd(SPM.swd) at line 200,
just after the code : SPM.swd = swd; at line 199.

[RC]

Getting more help

For help on SPM and other analysis topics, see AnalysisHelp

CbuImaging: SpmInformation (last edited 2013-04-24 13:41:20 by TiborAuer)