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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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| * 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. * SpmPlottingAdjustedData * DisplaySlices - display multiple image slices with activation data using matlab / SPM * Changing the location of images in an SPM design with SpmAnaCd * SpmTips - not otherwise classified tips and fixes * TrimmingImages using SPM = Automating SPM = * [:AutomaticAnalysisIntroduction:aa] - automating SPM analyses * SpmBatch - batching SPM jobs = Programming with SPM = * SpmGraphics - using the SPM output graphics for making figures * BasicProgrammingWithSpm = Benchmarking SPM = |
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| * 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. * SpmPlottingAdjustedData * SpmGraphics - using the SPM output graphics for making figures * DisplaySlices - display multiple image slices with activation data using matlab / SPM * TrimmingImages using SPM * Changing the location of images in an SPM design with SpmAnaCd * SpmTips - not otherwise classified tips and fixes * [http://www-psych.stanford.edu/~kalina/SPM99/ Kalina Christoff's SPM99 page] - a variety of interesting programs, protocols and discussions. * SpmManuals * [http://www.fil.ion.ucl.ac.uk/spm/course/ SPM course notes] * Rik Henson's SpmMiniCourse2005 * CBU SpmMiniCourse2007 |
* 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
SpmVersions - and how to launch them at the CBU
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.
DisplaySlices - display multiple image slices with activation data using matlab / SPM
Changing the location of images in an SPM design with SpmAnaCd
SpmTips - not otherwise classified tips and fixes
TrimmingImages using SPM
Automating SPM
[:AutomaticAnalysisIntroduction:aa] - automating SPM analyses
SpmBatch - batching SPM jobs
Programming with SPM
SpmGraphics - using the SPM output graphics for making figures
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
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 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.)
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